3HG7 | pdb_00003hg7

CRYSTAL STRUCTURE OF D-isomer specific 2-hydroxyacid dehydrogenase family protein from Aeromonas salmonicida subsp. salmonicida A449

• PDB DOI: https://doi.org/10.2210/pdb3HG7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aeromonas salmonicida subsp. salmonicida A449
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-05-13 Released: 2009-05-26 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Morano, C., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.264 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.228 (Depositor) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

CRYSTAL STRUCTURE OF D-isomer specific 2-hydroxyacid dehydrogenase family protein from Aeromonas salmonicida subsp. salmonicida A449

Malashkevich, V.N., Toro, R., Morano, C., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 36.59 kDa 
• Atom Count: 2,715 
• Modeled Residue Count: 310 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-isomer specific 2-hydroxyacid dehydrogenase family protein	A	324	Aeromonas salmonicida subsp. salmonicida A449	Mutation(s): 1  Gene Names: ASA_0563
UniProt
Find proteins for A4SIK7 (Aeromonas salmonicida (strain A449)) Explore A4SIK7  Go to UniProtKB:  A4SIK7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.264 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.228 (Depositor) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.055	α = 90
b = 117.055	β = 90
c = 64.336	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Malashkevich, V.N., Toro, R., Morano, C., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2012-10-24
  Changes: Structure summary
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2021-10-13
  Changes: Database references
• Version 1.7: 2024-02-21
  Changes: Data collection