5TSD | pdb_00005tsd

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

• PDB DOI: https://doi.org/10.2210/pdb5TSD/pdb

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


• Deposited: 2016-10-28 Released: 2016-11-16 
• Deposition Author(s): Matelska, D., Shabalin, I.G., Kutner, J., Handing, K.B., Gasiorowska, O.A., Cooper, D.R., 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: 1.90 Å
• R-Value Free: 
  0.198 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.155 (Depositor) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

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

Matelska, D., Shabalin, I.G., Kutner, J., Handing, K.B., Gasiorowska, O.A., Cooper, D.R., 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: 73.26 kDa 
• Atom Count: 5,598 
• Modeled Residue Count: 632 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable hydroxyacid dehydrogenase protein	A, B	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], E [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
OXD	D [auth A], F [auth B]	OXALIC ACID C2 H2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.198 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.155 (Depositor) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.945	α = 90
b = 70.124	β = 90
c = 126.615	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
HKL-3000	phasing
HKL-3000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-11-16 
Deposition Author(s): Matelska, D., Shabalin, I.G., Kutner, J., Handing, K.B., Gasiorowska, O.A., Cooper, D.R., 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	--

Revision History  

• Version 1.0: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.4: 2023-10-04
  Changes: Data collection, Refinement description