5TX7

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.230
R-Value Work: 0.174
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72C72 Go to UniProtKB: Q72C72
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q72C72
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.230
R-Value Work: 0.174
R-Value Observed: 0.177
Space Group: C 2 2 2₁
Diffraction Data: https://doi.org/10.18430/M35TX7

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-12-07

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

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

Revision History (Full details and data files)

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

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5TX7

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)