4N18

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase family protein from Klebsiella pneumoniae 342

• PDB DOI: https://doi.org/10.2210/pdb4N18/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Klebsiella pneumoniae 342
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-10-03 Released: 2013-10-16 
• Deposition Author(s): Bacal, P., Shabalin, I.G., Cooper, D.R., Majorek, K.A., Osinski, T., Hillerich, B.S., Hammonds, J., Nawar, A., Stead, M., Chowdhury, S., Gizzi, A., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.220 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase family protein from Klebsiella pneumoniae 342

Bacal, P., Shabalin, I.G., Cooper, D.R., Majorek, K.A., Osinski, T., Hillerich, B.S., Hammonds, J., Nawar, A., Stead, M., Chowdhury, S., Gizzi, A., Bonanno, J., Seidel, R., Almo, S.C., 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: 37.63 kDa 
• Atom Count: 2,543 
• Modelled Residue Count: 311 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-isomer specific 2-hydroxyacid dehydrogenase family protein	A	332	Klebsiella pneumoniae 342	Mutation(s): 0  Gene Names: KPK_1152
UniProt
Find proteins for B5XVG7 (Klebsiella pneumoniae (strain 342)) Explore B5XVG7  Go to UniProtKB:  B5XVG7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE4	B [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.220 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M36P46

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.567	α = 90
b = 76.567	β = 90
c = 101.281	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-16 
Deposition Author(s): Bacal, P., Shabalin, I.G., Cooper, D.R., Majorek, K.A., Osinski, T., Hillerich, B.S., Hammonds, J., Nawar, A., Stead, M., Chowdhury, S., Gizzi, A., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2024-10-16
  Changes: Data collection, Structure summary