5VG6 | pdb_00005vg6

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2 in complex with NADPH and MES.

PDB DOI: https://doi.org/10.2210/pdb5VG6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Xanthobacter versatilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-04-10 Released: 2017-04-26
Deposition Author(s): Lipowska, J., Shabalin, I.G., Kutner, J., Gasiorowska, O.A., 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: 2.20 Å
R-Value Free:
0.233 (Depositor), 0.237 (DCC)
R-Value Work:
0.200 (Depositor), 0.203 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2 in complex with NADPH and MES.

Lipowska, J., Shabalin, I.G., Almo, S.C., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 381.03 kDa
Atom Count: 25,838
Modeled Residue Count: 2,992
Deposited Residue Count: 3,410
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	341	Xanthobacter versatilis	Mutation(s): 0 Gene Names: Xaut_2571
UniProt
Find proteins for A7IIH0 (Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)) Explore A7IIH0 Go to UniProtKB: A7IIH0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7IIH0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain BA [auth J] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain X [auth G] SDF format, chain Y [auth H] SDF format, chain Z [auth I] MOL2 format, chain BA [auth J] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth H] MOL2 format, chain Z [auth I] mmCIF format, chain BA [auth J] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth H] mmCIF format, chain Z [auth I]	BA [auth J] K [auth A] N [auth B] P [auth C] R [auth D] BA [auth J], K [auth A], N [auth B], P [auth C], R [auth D], T [auth E], V [auth F], X [auth G], Y [auth H], Z [auth I]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain BA [auth J] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth I] Interactions & Density Focus chain BA [auth J] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth I]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain CA [auth J] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain W [auth F] SDF format, chain U [auth E] MOL2 format, chain AA [auth I] MOL2 format, chain CA [auth J] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] mmCIF format, chain AA [auth I] mmCIF format, chain CA [auth J] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E]	AA [auth I] CA [auth J] L [auth A] M [auth A] O [auth B] AA [auth I], CA [auth J], L [auth A], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.233 (Depositor), 0.237 (DCC)
R-Value Work: 0.200 (Depositor), 0.203 (DCC)
R-Value Observed: 0.201 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.514	α = 90
b = 311.036	β = 90
c = 98.977	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-04-26

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: 2017-04-26
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Refinement description
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description