Macromolecule Content

Total Structure Weight: 196.45 kDa
Atom Count: 14,009
Modelled Residue Count: 1,612
Deposited Residue Count: 1,764
Unique protein chains: 1

3N2B

1.8 Angstrom Resolution Crystal Structure of Diaminopimelate Decarboxylase (lysA) from Vibrio cholerae.

PDB DOI: 10.2210/pdb3N2B/pdb

Classification: LYASE
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-05-17 Released: 2010-06-09
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.219
R-Value Work: 0.183
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

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

Literature

1.8 Angstrom Resolution Crystal Structure of Diaminopimelate Decarboxylase (lysA) from Vibrio cholerae.

Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., 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
Diaminopimelate decarboxylase	A, B, C, D	441	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: lysA, VC_0125 EC: 4.1.1.20
UniProt
Find proteins for Q9KVL7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVL7 Go to UniProtKB: Q9KVL7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KVL7
Protein Feature View 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 F [auth C] SDF format, chain H [auth D] SDF format, chain E [auth A] SDF format, chain G [auth C] MOL2 format, chain F [auth C] MOL2 format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C]	E [auth A], F [auth C], G [auth C], H [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.219
R-Value Work: 0.183
R-Value Observed: 0.184
Space Group: P 1
Diffraction Data DOI: 10.18430/M33N2B

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.394	α = 105.31
b = 80.329	β = 93.62
c = 118.693	γ = 90.52

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-06-09

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-06-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
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.