3N2B | pdb_00003n2b

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

• PDB DOI: https://doi.org/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.219 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth C], G [auth C], H [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.219 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33n2b

Space Group: P 1

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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description