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BMRB: 15381

2JSX

Solution structure of the E. coli Tat proofreading chaperone protein NapD

Authors

Spronk, C.A.E.M., Vuister, G.W., Sargent, F.

Assembly

NapD

Entity

1. NapD (polymer, Thiol state: all free), 95 monomers, 10534.49 Da Detail

MHTNWQVCSL VVQAKSERIS DISTQLNAFP GCEVAVSDAP SGQLIVVVEA EDSETLIQTI ESVRNVEGVL AVSLVYHQQE EQGEETPRSH HHHHH

Formula weight

10534.49 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 89.5 %, Completeness: 77.7 %, Completeness (bb): 74.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.7 % (820 of 1055)	83.9 % (453 of 540)	67.9 % (279 of 411)	84.6 % (88 of 104)
Backbone	74.3 % (419 of 564)	87.4 % (167 of 191)	61.6 % (173 of 281)	85.9 % (79 of 92)
Sidechain	82.6 % (481 of 582)	81.9 % (286 of 349)	84.2 % (186 of 221)	75.0 % (9 of 12)
Aromatic	48.4 % (30 of 62)	48.4 % (15 of 31)	46.7 % (14 of 30)	100.0 % (1 of 1)
Methyl	100.0 % (118 of 118)	100.0 % (59 of 59)	100.0 % (59 of 59)

1. NapD

MHTNWQVCSL VVQAKSERIS DISTQLNAFP GCEVAVSDAP SGQLIVVVEA EDSETLIQTI ESVRNVEGVL AVSLVYHQQE EQGEETPRSH HHHHH

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Temperature 298 K, pH 7.4, Details Buffer conditions were: 20 mM deuterated Tris (pH 7.4), 1 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	NapD	[U-100% 13C; U-100% 15N]		0.5 mM
2	deuterated Tris			20 mM
3	DTT			1 mM

LACS Plot; CA

Referencing offset: -0.15 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.15 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2007-08-15

Citation

Structural diversity in twin-arginine signal peptide-binding proteins
Maillard, J., Spronk, C.A.E.M., Buchanan, G., Lyall, V., Richardson, D.J., Palmer, T., Vuister, G.W., Sargent, F.
Proc. Natl. Acad. Sci. U. S. A. (2007), 104, 15641-15646, PubMed 17901208 , DOI 10.1073/pnas.0703967104 , Abstract

Related entities 1. NapD, : 1 : 3 : 1 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz Triple resonance experiments

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 298 K, pH 7.4, Details Buffer conditions were: 20 mM deuterated Tris (pH 7.4), 1 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	NapD	[U-100% 13C; U-100% 15N]		0.5 mM
2	deuterated Tris			20 mM
3	DTT			1 mM

2 3D HNCACB

Instrument

Varian INOVA - 600 MHz Triple resonance experiments

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 298 K, pH 7.4, Details Buffer conditions were: 20 mM deuterated Tris (pH 7.4), 1 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	NapD	[U-100% 13C; U-100% 15N]		0.5 mM
2	deuterated Tris			20 mM
3	DTT			1 mM

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz Triple resonance experiments

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 298 K, pH 7.4, Details Buffer conditions were: 20 mM deuterated Tris (pH 7.4), 1 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	NapD	[U-100% 13C; U-100% 15N]		0.5 mM
2	deuterated Tris			20 mM
3	DTT			1 mM

4 3D HBHA(CBCACO)NH

Instrument

Varian INOVA - 600 MHz Triple resonance experiments

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 298 K, pH 7.4, Details Buffer conditions were: 20 mM deuterated Tris (pH 7.4), 1 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	NapD	[U-100% 13C; U-100% 15N]		0.5 mM
2	deuterated Tris			20 mM
3	DTT			1 mM

5 3D HN(CA)HA

Instrument

Varian INOVA - 600 MHz Triple resonance experiments

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 298 K, pH 7.4, Details Buffer conditions were: 20 mM deuterated Tris (pH 7.4), 1 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	NapD	[U-100% 13C; U-100% 15N]		0.5 mM
2	deuterated Tris			20 mM
3	DTT			1 mM

6 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz Triple resonance experiments

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 298 K, pH 7.4, Details Buffer conditions were: 20 mM deuterated Tris (pH 7.4), 1 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	NapD	[U-100% 13C; U-100% 15N]		0.5 mM
2	deuterated Tris			20 mM
3	DTT			1 mM

7 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz Triple resonance experiments

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 298 K, pH 7.4, Details Buffer conditions were: 20 mM deuterated Tris (pH 7.4), 1 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	NapD	[U-100% 13C; U-100% 15N]		0.5 mM
2	deuterated Tris			20 mM
3	DTT			1 mM

8 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz Triple resonance experiments

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 298 K, pH 7.4, Details Buffer conditions were: 20 mM deuterated Tris (pH 7.4), 1 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	NapD	[U-100% 13C; U-100% 15N]		0.5 mM
2	deuterated Tris			20 mM
3	DTT			1 mM

9 3D (H)CCH-TOCSY

Instrument

Varian INOVA - 600 MHz Triple resonance experiments

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 298 K, pH 7.4, Details Buffer conditions were: 20 mM deuterated Tris (pH 7.4), 1 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	NapD	[U-100% 13C; U-100% 15N]		0.5 mM
2	deuterated Tris			20 mM
3	DTT			1 mM

10 3D H(C)CH-TOCSY

Instrument

Varian INOVA - 600 MHz Triple resonance experiments

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 298 K, pH 7.4, Details Buffer conditions were: 20 mM deuterated Tris (pH 7.4), 1 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	NapD	[U-100% 13C; U-100% 15N]		0.5 mM
2	deuterated Tris			20 mM
3	DTT			1 mM

11 2D 1H-13C HSQC constant time

Instrument

Varian INOVA - 600 MHz Triple resonance experiments

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 298 K, pH 7.4, Details Buffer conditions were: 20 mM deuterated Tris (pH 7.4), 1 mM DTT

#	Name	Isotope labeling	Type	Concentration
7	NapD	[U-10% 13C; U-100% 15N]		0.5 mM
8	deuterated Tris			20 mM
9	DTT			1 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15381_2jsx.nef
Input source #2: Coordindates	2jsx.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-----
MHTNWQVCSLVVQAKSERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLIQTIESVRNVEGVLAVSLVYHQQEEQGEETPRSHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHTNWQVCSLVVQAKSERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLIQTIESVRNVEGVLAVSLVYHQQEEQGEETPRSHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	95	0	0	100.0

Content subtype: combined_15381_2jsx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	794		88.4 (chain: A, length: 95)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2245 (1)	noe	88.4 (chain: A, length: 95)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	119 (119)	.	81.1 (chain: A, length: 95)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 88.4%
- Total number of assignments
  - ¹H chemical shifts: 443
  - ¹³C chemical shifts: 266
  - ¹⁵N chemical shifts: 85
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 88.4%
- Total number of restraints: 2244
- Weight of restraints: 1.0 (2244)
- Potential type of restraints: square-well-parabolic (2244)
- Range of distance target values: 1.3, 2.85 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 81.1%
- Total number of restraints: 119
- Total number of restraints per polymer type: 119
- Weight of restraints: 1.0 (119)
- Potential type of restraints: square-well-parabolic (119)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Escherichia coli, metalloenzyme assembly chaperone, NapD protein, periplasmic nitrate reductase system, Tat proofreading chaperone, twin-arginine transport system