3GUY

Crystal structure of a short-chain dehydrogenase/reductase from Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb3GUY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio parahaemolyticus AQ3810
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-03-30 Released: 2009-04-14 
• Deposition Author(s): Patskovsky, Y., Bonanno, J.B., Freeman, J., Bain, K.T., Miller, S., Sampathkumar, P., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.249 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Crystal structure of a short-chain dehydrogenase/reductase from Vibrio parahaemolyticus

Patskovsky, Y., Bonanno, J.B., Freeman, J., Bain, K.T., Miller, S., Sampathkumar, P., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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 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: 200.27 kDa 
• Atom Count: 13,319 
• Modelled Residue Count: 1,685 
• Deposited Residue Count: 1,840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A, B, C, D, E, F, G, H	230	Vibrio parahaemolyticus AQ3810	Mutation(s): 2  Gene Names: A79_5576

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.249 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.814	α = 72.38
b = 71.315	β = 89.39
c = 93.075	γ = 74.3

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-14 
Deposition Author(s): Patskovsky, Y., Bonanno, J.B., Freeman, J., Bain, K.T., Miller, S., Sampathkumar, P., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.5: 2021-10-13
  Changes: Database references
• Version 1.6: 2024-02-21
  Changes: Data collection