Macromolecule Content

Total Structure Weight: 77.56 kDa
Atom Count: 5,685
Modelled Residue Count: 664
Deposited Residue Count: 692
Unique protein chains: 1

3N9I

Crystal structure of tryptophanyl-tRNA synthetase from Yersinia pestis CO92

PDB DOI: https://doi.org/10.2210/pdb3N9I/pdb

Classification: LIGASE
Organism(s): Yersinia pestis CO92
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2010-05-30 Released: 2010-07-21
Deposition Author(s): Nocek, B., Maltseva, N., Papazisi, L., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.206
R-Value Work: 0.167
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of tryptophanyl-tRNA synthetase from Yersinia pestis CO92

Nocek, B., Maltseva, N., Papazisi, L., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophanyl-tRNA synthetase	A, B	346	Yersinia pestis CO92	Mutation(s): 0 Gene Names: trpS, YPO0157, y3940, YP_0159 EC: 6.1.1.2
UniProt
Find proteins for Q8ZJF2 (Yersinia pestis) Explore Q8ZJF2 Go to UniProtKB: Q8ZJF2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8ZJF2
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B]	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.206
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M33N9I

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.099	α = 90
b = 78.15	β = 90
c = 152.176	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-07-21

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-07-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-10-01
Changes: Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.