2QMA | pdb_00002qma

Crystal structure of glutamate decarboxylase domain of diaminobutyrate-pyruvate transaminase and L-2,4-diaminobutyrate decarboxylase from Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb2QMA/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-07-14 Released: 2007-07-31 
• Deposition Author(s): Osipiuk, J., Sather, A., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.209 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

X-ray crystal structure of glutamate decarboxylase domain of diaminobutyrate-pyruvate transaminase and L-2,4-diaminobutyrate decarboxylase from Vibrio parahaemolyticus.

Osipiuk, J., Sather, A., Gu, M., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 110.32 kDa 
• Atom Count: 7,843 
• Modeled Residue Count: 922 
• Deposited Residue Count: 994 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminobutyrate-pyruvate transaminase and L-2,4-diaminobutyrate decarboxylase	A, B	497	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 19  Gene Names: VP1942
UniProt
Find proteins for Q87NC6 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87NC6  Go to UniProtKB:  Q87NC6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.209 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.431	α = 90
b = 122.776	β = 95.74
c = 64.289	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-31 
Deposition Author(s): Osipiuk, J., Sather, A., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-07-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary