4XCV

Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH

PDB DOI: https://doi.org/10.2210/pdb4XCV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhizobium etli CFN 42
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-12-18 Released: 2014-12-31
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 Obadi, 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: 1.40 Å
R-Value Free: 0.177
R-Value Work: 0.149
R-Value Observed: 0.151

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH

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

To be published.

Macromolecule Content

Total Structure Weight: 36.41 kDa
Atom Count: 3,132
Modelled Residue Count: 317
Deposited Residue Count: 320
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADP-dependent 2-hydroxyacid dehydrogenase	A	320	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2KDT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP 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]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.177
R-Value Work: 0.149
R-Value Observed: 0.151
Space Group: P 4₁ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M38G6H

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.663	α = 90
b = 65.663	β = 90
c = 151.458	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
MOLREP	phasing
HKL-3000	data scaling
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2014-12-31

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: 2014-12-31
Type: Initial release
Version 1.1: 2015-01-28
Changes: Structure summary
Version 1.2: 2017-11-22
Changes: Derived calculations, Refinement description, Source and taxonomy, Structure summary
Version 1.3: 2019-12-04
Changes: Author supporting evidence
Version 1.4: 2022-04-13
Changes: Database references, Structure summary
Version 1.5: 2023-09-27
Changes: Data collection, Refinement description