BMRB Entry 15471

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PDB ID: 2jva
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15471
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR Structure of Peptidyl-tRNA hydrolase domain protein from Pseudomonas syringae pv. tomato:Northeast Structural Genomics Consortium Target PsR211

Deposition date:

2007-09-14

Original release date:

2007-10-12

Authors:

SINGARAPU, KIRAN KUMAR; SUKUMARAN, DINESH; PARISH, DAVID; ELETSKY, ALEX; ZHANG, QI; ZHAO, LI; JIANG, MEI; MAGLAQUI, MELISSA; XIAO, RONG; LIU, JINFENG; BARAN, MICHAEL; SWAPNA, G.V.T; HUANG, YUANPENG; ACTON, THOMAS; ROST, BURKHARD; MONTELIONE, GAETANO; SZYPERSKI, THOMAS

Citation:

Citation: SINGARAPU, KIRAN KUMAR; XIAO, RONG; ACTON, THOMAS; ROST, BURKHARD; MONTELIONE, GAETANO; SZYPERSKI, THOMAS. "NMR structure of the peptidyl-tRNA hydrolase domain from Pseudomonas syringae expands the structural coverage of the hydrolysis domains of class 1 peptide chain release factors" Proteins 71, 1027-1031 (2008).
PubMed: 18247350

Assembly members:

Assembly members:
Peptidyl-tRNA hydrolase domain protein, polymer, 108 residues, 12100.852 Da.

Natural source:

Natural source: Common Name: Pseudomonas Syringae pv.tomato Taxonomy ID: 317 Superkingdom: Bacteria Kingdom: not available Genus/species: Pseudomonas syringae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pEt21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Peptidyl-tRNA hydrolase domain protein: MLVISNNVHLPDAEIELTAI RAQGAGGQNVNKVSSAMHLR FDINASSLPPFYKERLLALN DSRITSDGVIVLKAQQYRTQ EQNRADALLRLSELIVNAAK LEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	446
15N chemical shifts	116
1H chemical shifts	762

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Peptidyl-tRNA hydrolase domain protein	1

Entities:

Entity 1, Peptidyl-tRNA hydrolase domain protein 108 residues - 12100.852 Da.

1

MET

LEU

VAL

ILE

SER

ASN

VAL

HIS

LEU

2

PRO

ASP

ALA

GLU

ILE

GLU

LEU

THR

ALA

ILE

3

ARG

ALA

GLN

GLY

ALA

GLY

GLN

ASN

VAL

4

ASN

LYS

VAL

SER

ALA

MET

HIS

LEU

ARG

5

PHE

ASP

ILE

ASN

ALA

SER

LEU

PRO

6

PHE

TYR

LYS

GLU

ARG

LEU

ALA

LEU

ASN

7

ASP

SER

ARG

ILE

THR

SER

ASP

GLY

VAL

ILE

8

VAL

LEU

LYS

ALA

GLN

TYR

ARG

THR

GLN

9

GLU

GLN

ASN

ARG

ALA

ASP

ALA

LEU

ARG

10

LEU

SER

GLU

LEU

ILE

VAL

ASN

ALA

LYS

11

LEU

GLU

HIS

Samples:

sample_1: Peptidyl-tRNA hydrolase domain protein, [U-100% 13C; U-100% 15N], 1.28 mM; CaCl2 5 mM; NaCl 100 mM; NH4OAc 20 mM; DTT 10 mM; NaN3 0.02%; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 100 mM; pH: 5.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
4,3D GFT CABCACONHN	sample_1	isotropic	sample_conditions_1
4,3D GFT HNNCABCA	sample_1	isotropic	sample_conditions_1
4,3D GFT HCCH COSY	sample_1	isotropic	sample_conditions_1
3D HCCH COSY	sample_1	isotropic	sample_conditions_1
4,3D GFT HABCABCONHN	sample_1	isotropic	sample_conditions_1
3D sim NOESY	sample_1	isotropic	sample_conditions_1

Software:

VNMRJ, Varian - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

XEASY, Bartels et al. - data analysis

TALOS, Cornilescu, Delaglio and Bax - data analysis

DYANA, Guntert, Mumenthaler and Wuthrich - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - chemical shift assignment

AutoAssign, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

AutoStruct, Huang, Tejero, Powers and Montelione - chemical shift assignment

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

Varian INOVA 750 MHz

PDB	2JVA
GB	EPN16620 KPW06216