3LVY | pdb_00003lvy

Crystal Structure of Carboxymuconolactone Decarboxylase Family Protein SMU.961 from Streptococcus mutans

• PDB DOI: https://doi.org/10.2210/pdb3LVY/pdb

• Classification: LYASE
• Organism(s): Streptococcus mutans
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-02-22 Released: 2010-03-09 
• Deposition Author(s): Kim, Y., Xu, X., Cui, H., Chin, S., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.236 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal Structure of Carboxymuconolactone Decarboxylase Family Protein SMU.961 from Streptococcus mutans

Kim, Y., Xu, X., Cui, H., Chin, S., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 137.31 kDa 
• Atom Count: 8,818 
• Modeled Residue Count: 1,086 
• Deposited Residue Count: 1,242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxymuconolactone decarboxylase family	A, B, C, D, E, F	207	Streptococcus mutans	Mutation(s): 0  Gene Names: SMU_961
UniProt
Find proteins for Q8DUG8 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DUG8  Go to UniProtKB:  Q8DUG8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	K [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	G [auth A], I [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
CL	H [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.236 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.996	α = 90
b = 73.741	β = 98.68
c = 183.708	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Kim, Y., Xu, X., Cui, H., Chin, S., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary