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BMRB: 18187

2LO0

Solution structure of the Get5 carboxyl domain from A. fumigatus

Authors

Chartron, J.W., VanderVelde, D.G., Rao, M., Clemons, W.M.

Assembly

Get5 carboxyl domain from A. fumigatus

Entity

1. Get5 carboxyl domain from A. fumigatus (polymer, Thiol state: not present), 75 monomers, 8248.954 × 2 Da Detail

SVDVAVSAGA GERASAEQKE SYEPPKPAVG PSGESVVATE AFWDDLQGFL EQRLKDYDEA NKLRVLFKEA WRSSF

Total weight

16497.908 Da

Max. entity weight

8248.954 Da

Source organism

Aspergillus fumigatus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.7 %, Completeness: 92.6 %, Completeness (bb): 96.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.6 % (786 of 849)	88.4 % (390 of 441)	97.0 % (321 of 331)	97.4 % (75 of 77)
Backbone	96.8 % (428 of 442)	95.4 % (144 of 151)	97.7 % (215 of 220)	97.2 % (69 of 71)
Sidechain	89.5 % (427 of 477)	84.8 % (246 of 290)	96.7 % (175 of 181)	100.0 % (6 of 6)
Aromatic	100.0 % (80 of 80)	100.0 % (40 of 40)	100.0 % (38 of 38)	100.0 % (2 of 2)
Methyl	92.9 % (65 of 70)	88.6 % (31 of 35)	97.1 % (34 of 35)

1. Get5

SVDVAVSAGA GERASAEQKE SYEPPKPAVG PSGESVVATE AFWDDLQGFL EQRLKDYDEA NKLRVLFKEA WRSSF

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
6	Get5	[U-100% 15N]	2.5 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium azide	natural abundance	0.02 %
9	polyacrylamide	natural abundance	5 %
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1, Details 20 mM sodium phosphate, 0.02% sodium azide, 0.1 mg/ml trimethylsilyl propanoic acid

#	Name	Isotope labeling	Concentration
12	Get5	[U-100% 15N]	2.5 mM
13	sodium phosphate	natural abundance	20 mM
14	sodium azide	natural abundance	0.02 %
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
17	Get5	natural abundance	4 mM
18	Get5	[U-100% 13C; U-100% 15N]	2 mM
19	sodium phosphate	natural abundance	20 mM
20	sodium azide	natural abundance	0.02 %
21	H2O	natural abundance	90 %
22	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.255145
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: -0.13 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.255145
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: -0.13 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.255145
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.255145
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: -0.15 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2LO0, Strand ID: A, B Detail

Release date

2012-02-09

Citation

Get5 carboxyl-terminal domain is a novel dimerization motif that tethers an extended Get4/Get5 complex
Chartron, J.W., Vandervelde, D.G., Rao, M., Clemons, W.M.
J. Biol. Chem. (2012), 287, 8310-8317, PubMed 22262836 , DOI 10.1074/jbc.M111.333252 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 18186 released on 2012-02-09
Title Solution structure of the Get5 carboxyl domain from S. cerevisiae

Related entities 1. Get5 carboxyl domain from A. fumigatus, : 1 : 3 entities Detail

Experiments performed 19 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

3 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

4 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

5 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

6 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

7 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

8 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

9 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

10 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

11 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

12 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

13 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

14 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

15 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	Get5	[U-100% 13C; U-100% 15N]	3.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

16 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1, Details 20 mM sodium phosphate, 0.02% sodium azide, 0.1 mg/ml trimethylsilyl propanoic acid

#	Name	Isotope labeling	Concentration
12	Get5	[U-100% 15N]	2.5 mM
13	sodium phosphate	natural abundance	20 mM
14	sodium azide	natural abundance	0.02 %
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

17 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
6	Get5	[U-100% 15N]	2.5 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium azide	natural abundance	0.02 %
9	polyacrylamide	natural abundance	5 %
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %

18 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
12	Get5	[U-100% 15N]	2.5 mM
13	sodium phosphate	natural abundance	20 mM
14	sodium azide	natural abundance	0.02 %
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

19 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1

#	Name	Isotope labeling	Concentration
17	Get5	natural abundance	4 mM
18	Get5	[U-100% 13C; U-100% 15N]	2 mM
19	sodium phosphate	natural abundance	20 mM
20	sodium azide	natural abundance	0.02 %
21	H2O	natural abundance	90 %
22	D2O	natural abundance	10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18187_2lo0.nef
Input source #2: Coordindates	2lo0.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--160-------170-------180-------190-------200-------210-------220-------230
SVDVAVSAGAGERASAEQKESYEPPKPAVGPSGESVVATEAFWDDLQGFLEQRLKDYDEANKLRVLFKEAWRSSF
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SVDVAVSAGAGERASAEQKESYEPPKPAVGPSGESVVATEAFWDDLQGFLEQRLKDYDEANKLRVLFKEAWRSSF
--------10--------20--------30--------40--------50--------60--------70-----

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--160-------170-------180-------190-------200-------210-------220-------230
SVDVAVSAGAGERASAEQKESYEPPKPAVGPSGESVVATEAFWDDLQGFLEQRLKDYDEANKLRVLFKEAWRSSF
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SVDVAVSAGAGERASAEQKESYEPPKPAVGPSGESVVATEAFWDDLQGFLEQRLKDYDEANKLRVLFKEAWRSSF
--------10--------20--------30--------40--------50--------60--------70-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	75	0	0	100.0
B	B	75	0	0	100.0

Content subtype: combined_18187_2lo0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	774		98.7 (chain: A, length: 75)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2964 (1)	noe	60.0 (chain: A, length: 75), 60.0 (chain: B, length: 75)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	96 (1)	hbond	44.0 (chain: A, length: 75), 44.0 (chain: B, length: 75)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	152 (152)	.	54.7 (chain: A, length: 75), 54.7 (chain: B, length: 75)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	70 (70)	.	46.7 (chain: A, length: 75), 46.7 (chain: B, length: 75)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 378
  - ¹³C chemical shifts: 321
  - ¹⁵N chemical shifts: 75
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	441	378	85.7
¹³C chemical shifts	331	321	97.0
¹⁵N chemical shifts	81	75	92.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	151	143	94.7
¹³C chemical shifts	150	146	97.3
¹⁵N chemical shifts	71	69	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	290	235	81.0
¹³C chemical shifts	181	175	96.7
¹⁵N chemical shifts	10	6	60.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	29	82.9
¹³C chemical shifts	35	34	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	40	40	100.0
¹³C chemical shifts	38	38	100.0
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 60.0%
  - Entity_assembly_ID: B, Chain length: 75, Sequence coverage: 60.0%
- Total number of restraints: 2964
- Weight of restraints: 1.0 (2964)
- Potential type of restraints: square-well-parabolic (2964)
- Range of distance target values: 1.91, 4.35 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 44.0%
    - Entity_assembly_ID: B, Chain length: 75, Sequence coverage: 44.0%
  - Total number of restraints: 96
  - Weight of restraints: 1.0 (96)
  - Potential type of restraints: square-well-parabolic (96)
  - Range of distance target values: 2.05, 3.05 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 54.7%
  - Entity_assembly_ID: B, Chain length: 75, Sequence coverage: 54.7%
- Total number of restraints: 152
- Total number of restraints per polymer type: 152
- Weight of restraints: 1.0 (152)
- Potential type of restraints: square-well-parabolic (152)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 46.7%
  - Entity_assembly_ID: B, Chain length: 75, Sequence coverage: 46.7%
- Total number of restraints: 70
- Potential type of restraints: undefined (70)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords DIMER, GET, HOMODIMER, MDY2, PROTEIN

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Found 1 Document (0.681 seconds)

BMRB: 18187

Sample #1

Sample #2

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Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Get5 carboxyl domain from A. fumigatus, : 1 : 3 entities Detail

Experiments performed 19 experiments Detail

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NMR combined restraints 6 contents Detail