7E6O | pdb_00007e6o

Crystal structure of polyol dehydrogenase from Paracoccus denitrificans

• PDB DOI: https://doi.org/10.2210/pdb7E6O/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Paracoccus denitrificans PD1222
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-02-22 Released: 2022-03-02 
• Deposition Author(s): Sha, F., Zheng, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of polyol dehydrogenase from Paracoccus denitrificans

Sha, F., Zheng, Y.C., Gao, J.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 111.12 kDa 
• Atom Count: 7,684 
• Modeled Residue Count: 987 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A [auth C], B [auth A], C [auth B], D	264	Paracoccus denitrificans PD1222	Mutation(s): 0  Gene Names: Pden_4841
UniProt
Find proteins for A1BBK7 (Paracoccus denitrificans (strain Pd 1222)) Explore A1BBK7  Go to UniProtKB:  A1BBK7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.71	α = 90
b = 86.892	β = 90
c = 134.807	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Sha, F., Zheng, Y.C.

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description