3DB2 | pdb_00003db2

Crystal structure of a putative nadph-dependent oxidoreductase (dhaf_2064) from desulfitobacterium hafniense dcb-2 at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3DB2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Desulfitobacterium hafniense DCB-2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-30 Released: 2008-06-24 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.174 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.140 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Literature

Crystal structure of putative NADPH-dependent oxidoreductase (ZP_01370612.1) from DESULFITOBACTERIUM HAFNIENSE DCB-2 at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

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 Evidence: gel filtration

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 119.91 kDa 
• Atom Count: 8,697 
• Modeled Residue Count: 1,036 
• Deposited Residue Count: 1,062 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative NADPH-dependent oxidoreductase	A, B, C	354	Desulfitobacterium hafniense DCB-2	Mutation(s): 0  Gene Names: ZP_01370612.1, Dhaf_4026
UniProt
Find proteins for B8FRW3 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2)) Explore B8FRW3  Go to UniProtKB:  B8FRW3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth C], E [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.174 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.140 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33DB2

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.616	α = 90
b = 104.616	β = 90
c = 173.372	γ = 120

Software Package:

Software Name	Purpose
SHELXL-97	refinement
PHENIX	refinement
SHELX	phasing
SHELX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing
MolProbity	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-24 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-06-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2014-11-12
  Changes: Structure summary
• Version 1.3: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.6: 2024-10-30
  Changes: Data collection, Structure summary