5TNX | pdb_00005tnx

Crystal structure of Alcohol dehydrogenase zinc-binding domain protein from Burkholderia ambifaria

• PDB DOI: https://doi.org/10.2210/pdb5TNX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia ambifaria MC40-6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-10-15 Released: 2016-11-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.172 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Alcohol dehydrogenase zinc-binding domain protein from Burkholderia ambifaria

Abendroth, J., Mayclin, S.J., Lorimer, D., Edwards, T.E.

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: 40.27 kDa 
• Atom Count: 3,070 
• Modeled Residue Count: 370 
• Deposited Residue Count: 383 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase zinc-binding domain protein	A	383	Burkholderia ambifaria MC40-6	Mutation(s): 0  Gene Names: BamMC406_6306
UniProt
Find proteins for B1Z4S6 (Burkholderia ambifaria (strain MC40-6)) Explore B1Z4S6  Go to UniProtKB:  B1Z4S6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.172 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35TNX

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.06	α = 90
b = 92.65	β = 90
c = 120.41	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description