8IJG

Crystal structure of alcohol dehydrogenase M5 from Burkholderia gladioli with NADP

• PDB DOI: https://doi.org/10.2210/pdb8IJG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia gladioli BSR3
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2023-02-27 Released: 2024-03-06 
• Deposition Author(s): Han, X., Mei, Z.L., Liu, W.D., Sun, Z.T., Ma, J.A.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.254 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

Starting Model: in silico

Literature

Crystal structure of alcohol dehydrogenase from Burkholderia gladioli with NADP

Han, X., Mei, Z.L., Liu, W.D., Sun, Z.T., Ma, J.A.

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: 106.73 kDa 
• Atom Count: 7,670 
• Modelled Residue Count: 997 
• Deposited Residue Count: 1,004 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative short-chain dehydrogenases/reductase family protein	A, B, C, D	251	Burkholderia gladioli BSR3	Mutation(s): 5  Gene Names: bgla_2g00620
UniProt
Find proteins for F2LIG4 (Burkholderia gladioli (strain BSR3)) Explore F2LIG4  Go to UniProtKB:  F2LIG4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.254 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.127	α = 90
b = 111.05	β = 90
c = 229.917	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Han, X., Mei, Z.L., Liu, W.D., Sun, Z.T., Ma, J.A.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release