5BQF | pdb_00005bqf

Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADP, HEPES and L(+)-tartaric acid

PDB DOI: https://doi.org/10.2210/pdb5BQF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhizobium etli CFN 42
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-05-29 Released: 2015-06-17
Deposition Author(s): Langner, K.M., Shabalin, I.G., Handing, K.B., Gasiorowska, O.A., Stead, M., Hillerich, B.S., Chowdhury, S., Hammonds, J., Zimmerman, M.D., Al Obaidi, N., Bonanno, J., Seidel, R., 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: 1.45 Å
R-Value Free:
0.165 (Depositor), 0.165 (DCC)
R-Value Work:
0.139 (Depositor), 0.138 (DCC)
R-Value Observed:
0.140 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADP, HEPES and L-tartaric acid

Langner, K.M., Shabalin, I.G., Handing, K.B., Gasiorowska, O.A., Chowdhury, S., Zimmerman, M.D., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 37.09 kDa
Atom Count: 3,181
Modeled Residue Count: 317
Deposited Residue Count: 322
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADP-dependent 2-hydroxyacid dehydrogenase	A	322	Rhizobium etli CFN 42	Mutation(s): 0 Gene Names: RHE_CH00179
UniProt
Find proteins for Q2KDT2 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42)) Explore Q2KDT2 Go to UniProtKB: Q2KDT2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2KDT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.165 (Depositor), 0.165 (DCC)
R-Value Work: 0.139 (Depositor), 0.138 (DCC)
R-Value Observed: 0.140 (Depositor)

Diffraction Data:

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.692	α = 90
b = 65.692	β = 90
c = 151.406	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	phasing
Coot	model building
MOLREP	phasing
HKL-3000	data scaling
HKL-3000	data reduction
HKL-3000	data collection

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-06-17

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	U54-GM094662

Revision History (Full details and data files)

Version 1.0: 2015-06-17
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2023-09-27
Changes: Data collection, Refinement description