3MY7 | pdb_00003my7

The Crystal Structure of the ACDH domain of an Alcohol Dehydrogenase from Vibrio parahaemolyticus to 2.25A

• PDB DOI: https://doi.org/10.2210/pdb3MY7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-10 Released: 2010-06-02 
• Deposition Author(s): Stein, A.J., Weger, A., Volkart, L., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.281 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

The Crystal Structure of the ACDH domain of an Alcohol Dehydrogenase from Vibrio parahaemolyticus to 2.25A

Stein, A.J., Weger, A., Volkart, L., Gu, M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 195.11 kDa 
• Atom Count: 11,963 
• Modeled Residue Count: 1,651 
• Deposited Residue Count: 1,808 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase/acetaldehyde dehydrogenase	A, B, C, D	452	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0  Gene Names: VP2121
UniProt
Find proteins for Q87MW0 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87MW0  Go to UniProtKB:  Q87MW0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth B], G [auth C], H [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.281 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.654	α = 90
b = 145.489	β = 105.81
c = 91.986	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
SHELX	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-02 
Deposition Author(s): Stein, A.J., Weger, A., Volkart, L., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary