3M2T | pdb_00003m2t

The crystal structure of dehydrogenase from Chromobacterium violaceum

• PDB DOI: https://doi.org/10.2210/pdb3M2T/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Chromobacterium violaceum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-03-08 Released: 2010-04-07 
• Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.231 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

The crystal structure of dehydrogenase from Chromobacterium violaceum

Zhang, Z., Burley, S.K., 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: 82.76 kDa 
• Atom Count: 5,702 
• Modeled Residue Count: 684 
• Deposited Residue Count: 718 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable dehydrogenase	A, B	359	Chromobacterium violaceum	Mutation(s): 1  Gene Names: CV_1407
UniProt
Find proteins for Q7NY68 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NY68  Go to UniProtKB:  Q7NY68

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	D [auth A], E [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.30 Å
• R-Value Free:  0.231 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.86	α = 90
b = 63.386	β = 90
c = 103.629	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-07 
Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Advisory, Database references, Derived calculations, Structure summary
• Version 1.3: 2021-10-06
  Changes: Advisory, Database references
• Version 1.4: 2024-10-16
  Changes: Data collection, Structure summary