BMRBj - BMREntryMaster

Found 1 Document (0.621 seconds)

BMRB: 15079

2JN0

Solution NMR structure of the ygdR protein from Escherichia coli. Northeast Structural Genomics target ER382A.

Authors

Rossi, P., Chen, C.X., Jiang, M., Cunningham, K., Ma, L., Xiao, R., Liu, J.C., Baran, M., Swapna, G., Acton, T.B., Rost, B., Montelione, G.T.

Assembly

ER382A

Entity

1. ER382A (polymer, Thiol state: all free), 61 monomers, 7039.622 Da Detail

MSSDYVMATK DGRMILTDGK PEIDDDTGLV SYHDQQGNAM QINRDDVSQI IERLEHHHHH H

Formula weight

7039.622 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

SIMULATED ANNEALING

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 82.0 %, Completeness: 71.6 %, Completeness (bb): 72.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.6 % (490 of 684)	71.5 % (254 of 355)	71.5 % (188 of 263)	72.7 % (48 of 66)
Backbone	72.8 % (265 of 364)	75.2 % (94 of 125)	71.5 % (128 of 179)	71.7 % (43 of 60)
Sidechain	71.4 % (269 of 377)	69.6 % (160 of 230)	73.8 % (104 of 141)	83.3 % (5 of 6)
Aromatic	40.9 % (18 of 44)	40.9 % (9 of 22)	40.9 % (9 of 22)
Methyl	100.0 % (54 of 54)	100.0 % (27 of 27)	100.0 % (27 of 27)

1. ER382A

MSSDYVMATK DGRMILTDGK PEIDDDTGLV SYHDQQGNAM QINRDDVSQI IERLEHHHHH H

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details PST ID ER382A.007 NC

#	Name	Isotope labeling	Type	Concentration
1	ER382A	[U-100% 13C; U-100% 15N]		1.17 mM
2	DTT	natural abundance		10 mM
3	CaCl2	natural abundance		5 mM
4	NaCl	natural abundance		0.1 M
5	MES	natural abundance		20 mM
6	sodium azide	natural abundance		0.02 %

LACS Plot; CA

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.24 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JN0, Strand ID: A Detail

Release date

2007-02-22

Citation

Solution NMR structure of the ygdR protein from Escherichia coli. Northeast Structural Genomics target ER382A
Rossi, P., Chen, C.X., Jiang, M., Cunningham, K., Ma, L., Xiao, R., Liu, J., Baran, M.C., Swapna, G., Acton, T.B., Rost, B., Montelione, G.T.

Related entities 1. ER382A, : 1 : 3 : 11 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details PST ID ER382A.007 NC

#	Name	Isotope labeling	Type	Concentration
1	ER382A	[U-100% 13C; U-100% 15N]		1.17 mM
2	DTT	natural abundance		10 mM
3	CaCl2	natural abundance		5 mM
4	NaCl	natural abundance		0.1 M
5	MES	natural abundance		20 mM
6	sodium azide	natural abundance		0.02 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details PST ID ER382A.007 NC

#	Name	Isotope labeling	Type	Concentration
1	ER382A	[U-100% 13C; U-100% 15N]		1.17 mM
2	DTT	natural abundance		10 mM
3	CaCl2	natural abundance		5 mM
4	NaCl	natural abundance		0.1 M
5	MES	natural abundance		20 mM
6	sodium azide	natural abundance		0.02 %

3 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details PST ID ER382A.007 NC

#	Name	Isotope labeling	Type	Concentration
1	ER382A	[U-100% 13C; U-100% 15N]		1.17 mM
2	DTT	natural abundance		10 mM
3	CaCl2	natural abundance		5 mM
4	NaCl	natural abundance		0.1 M
5	MES	natural abundance		20 mM
6	sodium azide	natural abundance		0.02 %

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details PST ID ER382A.007 NC

#	Name	Isotope labeling	Type	Concentration
1	ER382A	[U-100% 13C; U-100% 15N]		1.17 mM
2	DTT	natural abundance		10 mM
3	CaCl2	natural abundance		5 mM
4	NaCl	natural abundance		0.1 M
5	MES	natural abundance		20 mM
6	sodium azide	natural abundance		0.02 %

5 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details PST ID ER382A.007 NC

#	Name	Isotope labeling	Type	Concentration
1	ER382A	[U-100% 13C; U-100% 15N]		1.17 mM
2	DTT	natural abundance		10 mM
3	CaCl2	natural abundance		5 mM
4	NaCl	natural abundance		0.1 M
5	MES	natural abundance		20 mM
6	sodium azide	natural abundance		0.02 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details PST ID ER382A.007 NC

#	Name	Isotope labeling	Type	Concentration
1	ER382A	[U-100% 13C; U-100% 15N]		1.17 mM
2	DTT	natural abundance		10 mM
3	CaCl2	natural abundance		5 mM
4	NaCl	natural abundance		0.1 M
5	MES	natural abundance		20 mM
6	sodium azide	natural abundance		0.02 %

7 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details PST ID ER382A.007 NC

#	Name	Isotope labeling	Type	Concentration
1	ER382A	[U-100% 13C; U-100% 15N]		1.17 mM
2	DTT	natural abundance		10 mM
3	CaCl2	natural abundance		5 mM
4	NaCl	natural abundance		0.1 M
5	MES	natural abundance		20 mM
6	sodium azide	natural abundance		0.02 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details PST ID ER382A.007 NC

#	Name	Isotope labeling	Type	Concentration
1	ER382A	[U-100% 13C; U-100% 15N]		1.17 mM
2	DTT	natural abundance		10 mM
3	CaCl2	natural abundance		5 mM
4	NaCl	natural abundance		0.1 M
5	MES	natural abundance		20 mM
6	sodium azide	natural abundance		0.02 %

9 3D HN(CO)CACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details PST ID ER382A.007 NC

#	Name	Isotope labeling	Type	Concentration
1	ER382A	[U-100% 13C; U-100% 15N]		1.17 mM
2	DTT	natural abundance		10 mM
3	CaCl2	natural abundance		5 mM
4	NaCl	natural abundance		0.1 M
5	MES	natural abundance		20 mM
6	sodium azide	natural abundance		0.02 %

10 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details PST ID ER382A.007 NC

#	Name	Isotope labeling	Type	Concentration
1	ER382A	[U-100% 13C; U-100% 15N]		1.17 mM
2	DTT	natural abundance		10 mM
3	CaCl2	natural abundance		5 mM
4	NaCl	natural abundance		0.1 M
5	MES	natural abundance		20 mM
6	sodium azide	natural abundance		0.02 %

11 3D CCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details PST ID ER382A.007 NC

#	Name	Isotope labeling	Type	Concentration
1	ER382A	[U-100% 13C; U-100% 15N]		1.17 mM
2	DTT	natural abundance		10 mM
3	CaCl2	natural abundance		5 mM
4	NaCl	natural abundance		0.1 M
5	MES	natural abundance		20 mM
6	sodium azide	natural abundance		0.02 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15079_2jn0.nef
Input source #2: Coordindates	2jn0.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-
MSSDYVMATKDGRMILTDGKPEIDDDTGLVSYHDQQGNAMQINRDDVSQIIERLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSSDYVMATKDGRMILTDGKPEIDDDTGLVSYHDQQGNAMQINRDDVSQIIERLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	61	0	0	100.0

Content subtype: combined_15079_2jn0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	492		82.0 (chain: A, length: 61)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	659 (1)	noe	73.8 (chain: A, length: 61)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	20 (1)	hbond	19.7 (chain: A, length: 61)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	42 (42)	.	50.8 (chain: A, length: 61)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 82.0%
- Total number of assignments
  - ¹H chemical shifts: 254
  - ¹³C chemical shifts: 188
  - ¹⁵N chemical shifts: 50
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 73.8%
- Total number of restraints: 658
- Weight of restraints: 1.0 (658)
- Potential type of restraints: square-well-parabolic (658)
- Range of distance target values: 2.35, 3.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 19.7%
  - Total number of restraints: 20
  - Weight of restraints: 1.0 (20)
  - Potential type of restraints: square-well-parabolic (20)
  - Range of distance target values: 1.9, 2.85 (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: 61, Sequence coverage: 50.8%
- Total number of restraints: 42
- Total number of restraints per polymer type: 42
- Weight of restraints: 1.0 (42)
- Potential type of restraints: square-well-parabolic (42)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Lipoprotein, PSI-2