3R64 | pdb_00003r64

Crystal structure of a NAD-dependent benzaldehyde dehydrogenase from Corynebacterium glutamicum

• PDB DOI: https://doi.org/10.2210/pdb3R64/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Corynebacterium glutamicum ATCC 13032
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-21 Released: 2011-04-06 
• Deposition Author(s): Agarwal, R., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a NAD-dependent benzaldehyde dehydrogenase from Corynebacterium glutamicum

Agarwal, R., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 216.64 kDa 
• Atom Count: 13,674 
• Modeled Residue Count: 1,839 
• Deposited Residue Count: 2,032 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD dependent benzaldehyde dehydrogenase	A, B, C, D	508	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0  Gene Names: xylC, cg2953 EC: 1.2.1.28

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.92	α = 90
b = 99.826	β = 113.94
c = 160.975	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOLREP	phasing
CCP4	refinement
REFMAC	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Agarwal, R., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Refinement description