4N18 | pdb_00004n18

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 variicola 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.220 (Depositor), 0.224 (DCC)
R-Value Work:
0.181 (Depositor), 0.194 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 37.63 kDa
Atom Count: 2,543
Modeled Residue Count: 311
Deposited Residue Count: 332
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-isomer specific 2-hydroxyacid dehydrogenase family protein	A	332	Klebsiella variicola 342	Mutation(s): 0 Gene Names: KPK_1152
UniProt
Find proteins for B5XVG7 (Klebsiella variicola (strain 342)) Explore B5XVG7 Go to UniProtKB: B5XVG7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5XVG7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE4 Query on PE4 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]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CIT Query on CIT 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]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.224 (DCC)
R-Value Work: 0.181 (Depositor), 0.194 (DCC)
R-Value Observed: 0.183 (Depositor)

Diffraction Data:

Space Group: P 4₁ 2₁ 2

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-10-16

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

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