5TX7 | pdb_00005tx7

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Desulfovibrio vulgaris

• PDB DOI: https://doi.org/10.2210/pdb5TX7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nitratidesulfovibrio vulgaris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-15 Released: 2016-12-07 
• Deposition Author(s): Czub, M.P., Shabalin, I.G., Gasiorowska, O.A., Handing, K.B., Kutner, J., Cymborowski, M.T., Hennig, P.M., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Desulfovibrio vulgaris

Czub, M.P., Shabalin, I.G., Gasiorowska, O.A., Handing, K.B., Kutner, J., Cymborowski, M.T., Hennig, P.M., Bonanno, J., Almo, S.C., Minor, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.69 kDa 
• Atom Count: 5,058 
• Modeled Residue Count: 645 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-isomer specific 2-hydroxyacid dehydrogenase family protein	A, B	327	Nitratidesulfovibrio vulgaris	Mutation(s): 0  Gene Names: AAS95890.1 EC: 1.1.1
UniProt
Find proteins for Q72C72 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72C72  Go to UniProtKB:  Q72C72

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	E [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	C [auth A], D [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35TX7

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.109	α = 90
b = 117.107	β = 90
c = 135.84	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Czub, M.P., Shabalin, I.G., Gasiorowska, O.A., Handing, K.B., Kutner, J., Cymborowski, M.T., Hennig, P.M., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Database references, Structure summary
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.5: 2023-10-04
  Changes: Data collection, Refinement description