2GFF

Crystal Structure of Yersinia pestis LsrG

PDB DOI: https://doi.org/10.2210/pdb2GFF/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Yersinia pestis
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2006-03-21 Released: 2007-04-03
Deposition Author(s): de Carvalho-Kavanagh, M., Schafer, J., Lekin, T., Toppani, D., Chain, P., Lao, V., Motin, V., Garcia, E., Segelke, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.258
R-Value Work: 0.197
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of lsrG from Yersinia Pestis

de Carvalho-Kavanagh, M., Schafer, J., Lekin, T., Toppani, D., Coleman, M., Chain, P., Lao, V., Zemla, A., Motin, V., Garcia, E., Segelke, B.

To be published.

Macromolecule Content

Total Structure Weight: 24.98 kDa
Atom Count: 1,830
Modelled Residue Count: 197
Deposited Residue Count: 212
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LsrG Protein	A, B	106	Yersinia pestis	Mutation(s): 3 Gene Names: lsrG, YPO0407, y3774, YP_3774 EC: 5.3.1.32
UniProt
Find proteins for Q7CG46 (Yersinia pestis) Explore Q7CG46 Go to UniProtKB: Q7CG46
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7CG46
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.258
R-Value Work: 0.197
R-Value Observed: 0.200
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.174	α = 90
b = 56.174	β = 90
c = 119.397	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-04-03

Deposition Author(s):

de Carvalho-Kavanagh, M.

Revision History (Full details and data files)

Version 1.0: 2007-04-03
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description

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.