2Q0T | pdb_00002q0t

Crystal structure of a putative gamma-carboxymuconolactone decarboxylase subunit (bxe_b0980) from burkholderia xenovorans lb400 at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2Q0T/pdb

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


• Deposited: 2007-05-22 Released: 2007-06-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Crystal structure of putative gamma-carboxymuconolactone decarboxylase subunit (YP_554324.1) from Burkholderia xenovorans LB400 at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 87.96 kDa 
• Atom Count: 6,967 
• Modeled Residue Count: 756 
• Deposited Residue Count: 789 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative gamma-carboxymuconolactone decarboxylase subunit	A, B, C	263	Paraburkholderia xenovorans LB400	Mutation(s): 3  Gene Names: YP_554324.1, Bxeno_B2006, Bxe_B0980
UniProt
Find proteins for Q13LR5 (Paraburkholderia xenovorans (strain LB400)) Explore Q13LR5  Go to UniProtKB:  Q13LR5

Small Molecules

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: 1.70 Å
• R-Value Free:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32Q0T

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.3	α = 90
b = 83.11	β = 103.16
c = 99.26	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-06-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, 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
• Version 1.6: 2024-11-20
  Changes: Data collection, Structure summary