RCSB PDB - 4G2N: Crystal structure of putative D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding from Polaromonas sp. JS6 66

 4G2N

Crystal structure of putative D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding from Polaromonas sp. JS6 66


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.218 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of putative D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding from Polaromonas sp. JS6 66

Malashkevich, V.N.Bhosle, R.Toro, R.Hillerich, B.Gizzi, A.Garforth, S.Kar, A.Chan, M.K.Lafluer, J.Patel, H.Matikainen, B.Chamala, S.Lim, S.Celikgil, A.Villegas, G.Evans, B.Zenchek, W.Love, J.Fiser, A.Khafizov, K.Seidel, R.Bonanno, J.B.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
A, B, C, D
345Polaromonas sp. JS666Mutation(s): 0 
Gene Names: Bpro_5114
UniProt
Find proteins for Q120R1 (Polaromonas sp. (strain JS666 / ATCC BAA-500))
Explore Q120R1 
Go to UniProtKB:  Q120R1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ120R1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth B]
I [auth C]
J [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth B],
L [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.218 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.431α = 96.93
b = 68.158β = 90.68
c = 77.369γ = 94.38
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary