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BMRB: 18337

2LR0

SOLUTION NMR STRUCTURE OF DE NOVO DESIGNED PROTEIN, P-LOOP NTPASE FOLD, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR136

Authors

Liu, G., Koga, N., Koga, R., Xiao, R., Lee, H., Janjua, H., Kohan, E., Acton, T.B., Everett, J.K., Baker, D., Montelione, G.T.

Assembly

OR136

Entity

1. OR136 (polymer, Thiol state: not present), 134 monomers, 15959.14 Da Detail

MKILILINTN NDELIKKIKK EVENQGYQVR DVNDSDELKK EMKKLAEEKN FEKILIKSND KQLLKEMLEL ISKLGYKVFL LLADQDENEL EEFKRKIESQ GYEVRKVTDD EEALKIVREF MQKAGSLEHH HHHH

Formula weight

15959.14 Da

Exptl. method

solution NMR

Refine. method

distance geometry, simulated annealing, molecular dynamics

Data set

RDCs, assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 98.5 %, Completeness: 95.7 %, Completeness (bb): 95.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.7 % (1618 of 1690)	96.7 % (868 of 898)	94.6 % (609 of 644)	95.3 % (141 of 148)
Backbone	95.0 % (764 of 804)	96.0 % (261 of 272)	94.5 % (376 of 398)	94.8 % (127 of 134)
Sidechain	96.3 % (978 of 1016)	97.0 % (607 of 626)	94.9 % (357 of 376)	100.0 % (14 of 14)
Aromatic	76.1 % (67 of 88)	81.8 % (36 of 44)	70.5 % (31 of 44)
Methyl	100.0 % (148 of 148)	100.0 % (74 of 74)	100.0 % (74 of 74)

1. OR136

MKILILINTN NDELIKKIKK EVENQGYQVR DVNDSDELKK EMKKLAEEKN FEKILIKSND KQLLKEMLEL ISKLGYKVFL LLADQDENEL EEFKRKIESQ GYEVRKVTDD EEALKIVREF MQKAGSLEHH HHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.16309 mM OR136.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR136.001	[U-100% 13C; U-100% 15N]	1.16309 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.72 mM OR136.007, 90% H2O/10% D2O Alignment Media: Peg

#	Name	Isotope labeling	Concentration
6	OR136.007	[U-100% 13C; U-100% 15N]	0.72 mM
7	NaCl	natural abundance	100 mM
8	DTT	natural abundance	5 mM
9	NaN3	natural abundance	0.02 %
10	Tris-HCl pH 7.5	natural abundance	10 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.72 mM OR136.006, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	OR136.006	[U-100% 13C; U-100% 15N]	0.72 mM
12	NaCl	natural abundance	100 mM
13	DTT	natural abundance	5 mM
14	NaN3	natural abundance	0.02 %
15	Tris-HCl pH 7.5	natural abundance	10 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.08 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.14 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LR0, Strand ID: A Detail

RDC

91 RDC values in 1 lists
Field strength (¹H) 599.520 MHz, Pressure 1 atm, Temperature 298 K, pH 6.5 Detail

Release date

2012-04-15

Related entities 1. OR136, : 1 : 2 : 13 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.16309 mM OR136.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR136.001	[U-100% 13C; U-100% 15N]	1.16309 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM

2 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 6.5, Details 0.72 mM OR136.006, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	OR136.006	[U-100% 13C; U-100% 15N]	0.72 mM
12	NaCl	natural abundance	100 mM
13	DTT	natural abundance	5 mM
14	NaN3	natural abundance	0.02 %
15	Tris-HCl pH 7.5	natural abundance	10 mM

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.16309 mM OR136.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR136.001	[U-100% 13C; U-100% 15N]	1.16309 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.16309 mM OR136.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR136.001	[U-100% 13C; U-100% 15N]	1.16309 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.16309 mM OR136.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR136.001	[U-100% 13C; U-100% 15N]	1.16309 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.16309 mM OR136.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR136.001	[U-100% 13C; U-100% 15N]	1.16309 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM

7 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.16309 mM OR136.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR136.001	[U-100% 13C; U-100% 15N]	1.16309 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM

8 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz UGA for RDC measurement

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.72 mM OR136.007, 90% H2O/10% D2O Alignment Media: Peg

#	Name	Isotope labeling	Concentration
6	OR136.007	[U-100% 13C; U-100% 15N]	0.72 mM
7	NaCl	natural abundance	100 mM
8	DTT	natural abundance	5 mM
9	NaN3	natural abundance	0.02 %
10	Tris-HCl pH 7.5	natural abundance	10 mM

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.16309 mM OR136.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR136.001	[U-100% 13C; U-100% 15N]	1.16309 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18337_2lr0.nef
Input source #2: Coordindates	2lr0.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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MKILILINTNNDELIKKIKKEVENQGYQVRDVNDSDELKKEMKKLAEEKNFEKILIKSNDKQLLKEMLELISKLGYKVFLLLADQDENELEEFKRKIESQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKILILINTNNDELIKKIKKEVENQGYQVRDVNDSDELKKEMKKLAEEKNFEKILIKSNDKQLLKEMLELISKLGYKVFLLLADQDENELEEFKRKIESQ

-------110-------120-------130----
GYEVRKVTDDEEALKIVREFMQKAGSLEHHHHHH
||||||||||||||||||||||||||||||||||
GYEVRKVTDDEEALKIVREFMQKAGSLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	134	0	0	100.0

Content subtype: combined_18337_2lr0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1608		97.8 (chain: A, length: 134)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	5908 (1)	noe	96.3 (chain: A, length: 134)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	56 (1)	hbond	35.1 (chain: A, length: 134)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	230 (230)	.	95.5 (chain: A, length: 134)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 97.8%
- Total number of assignments
  - ¹H chemical shifts: 859
  - ¹³C chemical shifts: 609
  - ¹⁵N chemical shifts: 140
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
9	THR	HG1	5.789
58	SER	HG	5.159

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	898	857	95.4
¹³C chemical shifts	644	609	94.6
¹⁵N chemical shifts	152	140	92.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	272	258	94.9
¹³C chemical shifts	268	252	94.0
¹⁵N chemical shifts	134	126	94.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	626	599	95.7
¹³C chemical shifts	376	357	94.9
¹⁵N chemical shifts	18	14	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	78	100.0
¹³C chemical shifts	78	78	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	32	72.7
¹³C chemical shifts	44	31	70.5

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 96.3%
- Total number of restraints: 5890
- Weight of restraints: 1.0 (5890)
- Potential type of restraints: square-well-parabolic (5890)
- Range of distance target values: 2.15, 4.46 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- 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: 134, Sequence coverage: 35.1%
  - Total number of restraints: 56
  - Weight of restraints: 1.0 (56)
  - Potential type of restraints: square-well-parabolic (56)
  - Range of distance target values: 1.99, 2.99 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - 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: 134, Sequence coverage: 95.5%
- Total number of restraints: 230
- Total number of restraints per polymer type: 230
- Weight of restraints: 1.0 (230)
- Potential type of restraints: square-well-parabolic (230)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), PSI-Biology, Protein NMR, Protein Structure Initiative, Structural Genomics, Target OR136

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Found 1 Document (0.75 seconds)

BMRB: 18337

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. OR136, : 1 : 2 : 13 entities Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 5 contents Detail