4BMS | pdb_00004bms

Short chain alcohol dehydrogenase from Ralstonia sp. DSM 6428 in complex with NADPH

• PDB DOI: https://doi.org/10.2210/pdb4BMS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Ralstonia sp. DSMZ 6428
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-05-10 Released: 2014-03-19 
• Deposition Author(s): Man, H., Kulig, J., Rother, D., Grogan, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.293 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.272 (DCC) 
• R-Value Observed: 
  0.269 (Depositor) 

Literature

Structures of Alcohol Dehydrogenases from Ralstonia and Sphingobium Spp. Reveal the Molecular Basis for Their Recognition of 'Bulky-Bulky' Ketones

Man, H., Kedziora, K., Kulig, J., Frank, A., Lavandera, I., Gotor-Fernandez, V., Rother, D., Hart, S., Turkenburg, J.P., Grogan, G.

(2014) Top Catal 57: 356

• DOI: https://doi.org/10.1007/S11244-013-0191-2

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 165.03 kDa 
• Atom Count: 11,313 
• Modeled Residue Count: 1,487 
• Deposited Residue Count: 1,494 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE	A, B, C, D [auth E], E [auth F], F [auth K]	249	Ralstonia sp. DSMZ 6428	Mutation(s): 0  EC: 1.1.1.1
UniProt
Find proteins for C0IR58 (Ralstonia sp. DSMZ 6428) Explore C0IR58  Go to UniProtKB:  C0IR58

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	G [auth A], H [auth B], I [auth C], J [auth E], K [auth F], L [auth K]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.293 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.272 (DCC) 
• R-Value Observed: 0.269 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.26	α = 90
b = 135.62	β = 100.12
c = 93.58	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-19 
Deposition Author(s): Man, H., Kulig, J., Rother, D., Grogan, G.

Revision History  

• Version 1.0: 2014-03-19
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other