3R4I

Crystal structure of a Citrate lyase (Bxe_B2899) from BURKHOLDERIA XENOVORANS LB400 at 2.24 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a Citrate lyase (Bxe_B2899) from BURKHOLDERIA XENOVORANS LB400 at 2.24 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Citrate Lyase
A, B, C, D, E, F
A, B, C, D, E, F
339Paraburkholderia xenovorans LB400Mutation(s): 0 
Gene Names: Bxeno_B0128Bxe_B2899
EC: 4.1.3.6
UniProt
Find proteins for Q13S43 (Paraburkholderia xenovorans (strain LB400))
Explore Q13S43 
Go to UniProtKB:  Q13S43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13S43
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
O [auth C],
T [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth B],
J [auth B],
L [auth C],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
P [auth D],
Q [auth D],
R [auth D],
U [auth E],
V [auth E],
X [auth F],
Y [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth B],
N [auth C],
S [auth D],
W [auth E],
Z [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 3
  • Diffraction Data DOI: 10.18430/M33R4I Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.468α = 90
b = 148.468β = 90
c = 79.57γ = 120
Software Package:
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2023-02-01
    Changes: Database references, Derived calculations