4G9Q | pdb_00004g9q

Crystal structure of a 4-carboxymuconolactone decarboxylase

• PDB DOI: https://doi.org/10.2210/pdb4G9Q/pdb

• Classification: LYASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-07-24 Released: 2012-08-15 
• Deposition Author(s): Hickey, H.D., Mcgillick, B.E., Eswaramoorthy, S., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of a 4-carboxymuconolactone decarboxylase

Hickey, H.D., Mcgillick, B.E., Eswaramoorthy, S., Almo, S.C., Swaminathan, S.

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: 29.78 kDa 
• Atom Count: 1,998 
• Modeled Residue Count: 238 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-carboxymuconolactone decarboxylase	A	269	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: RA0292, SMa0559
UniProt
Find proteins for Q930A6 (Rhizobium meliloti (strain 1021)) Explore Q930A6  Go to UniProtKB:  Q930A6

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.345	α = 90
b = 104.345	β = 90
c = 63.191	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Hickey, H.D., Mcgillick, B.E., Eswaramoorthy, S., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary