5BQF

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.165 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 

Starting Model: experimental

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.

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: 37.09 kDa 
• Atom Count: 3,181 
• Modelled Residue Count: 317 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.165 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M3T885

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

Entry History & Funding Information

Deposition Data

• Released Date: 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)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54-GM094662

Revision History  

• 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