2QEU

Crystal structure of putative carboxymuconolactone decarboxylase (YP_555818.1) from Burkholderia xenovorans LB400 at 1.65 A resolution

• PDB DOI:  https://doi.org/10.2210/pdb2QEU/pdb

• Classification: LYASE
• Organism(s): Paraburkholderia xenovorans LB400
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-06-26 Released: 2007-07-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.180 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 

Literature

Crystal structure of Putative carboxymuconolactone decarboxylase (YP_555818.1) from Burkholderia xenovorans LB400 at 1.65 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 48.55 kDa 
• Atom Count: 3,764 
• Modelled Residue Count: 397 
• Deposited Residue Count: 423 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative carboxymuconolactone decarboxylase	A, B, C	141	Paraburkholderia xenovorans LB400	Mutation(s): 6  Gene Names: YP_555818.1, Bxeno_C0540, Bxe_C0569
UniProt
Find proteins for Q13HH1 (Paraburkholderia xenovorans (strain LB400)) Explore Q13HH1  Go to UniProtKB:  Q13HH1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	I [auth A], L [auth B], O [auth C]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	J [auth A], M [auth B], P [auth C], Q [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], N [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.180 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 
• Space Group: P 6₁ 2 2
• Diffraction Data: https://doi.org/10.18430/M32QEU

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.173	α = 90
b = 71.173	β = 90
c = 325.501	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-07-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations