3RQ1

Crystal Structure of Aminotransferase Class I and II from Veillonella parvula


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Aminotransferase Class I and II from Veillonella parvula

Kim, Y.Hatzos-Skintges, C.Clancy, S.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aminotransferase class I and IIA, B, C, D418Veillonella parvula DSM 2008Mutation(s): 0 
Gene Names: Vpar_1105
UniProt
Find proteins for D1BN29 (Veillonella parvula (strain ATCC 10790 / DSM 2008 / CCUG 5123 / JCM 12972 / NCTC 11810 / Te3))
Explore D1BN29 
Go to UniProtKB:  D1BN29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1BN29
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

Download Ideal Coordinates CCD File 
M [auth C]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
OAA
Query on OAA

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
O [auth C]
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth C],
E [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth C],
N [auth C],
P [auth C],
Q [auth D],
R [auth D],
S [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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: 2.20 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 
  • Space Group: P 1
  • Diffraction Data DOI: 10.18430/M33RQ1 Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.991α = 102.4
b = 81.057β = 101.37
c = 106.395γ = 102.95
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance