3E0R | pdb_00003e0r

Crystal structure of cppA protein from Streptococcus pneumoniae TIGR4

• PDB DOI: https://doi.org/10.2210/pdb3E0R/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-31 Released: 2008-08-19 
• Deposition Author(s): Nocek, B., Mulligan, R., Abdullah, J., Otwinowski, Z., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.256 (Depositor) 
• R-Value Work: 
  0.189 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal structure of cppA protein from Streptococcus pneumoniae TIGR4

Nocek, B., Mulligan, R., Abdullah, S., Otwinowski, Z., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 111.97 kDa 
• Atom Count: 8,192 
• Modeled Residue Count: 947 
• Deposited Residue Count: 976 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C3-degrading proteinase (CppA protein)	A, B, C, D	244	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: cppA, SP_1449
UniProt
Find proteins for Q9X4I9 (Streptococcus pneumoniae) Explore Q9X4I9  Go to UniProtKB:  Q9X4I9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A, B, C, D	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.256 (Depositor) 
• R-Value Work:  0.189 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.742	α = 90
b = 130.741	β = 90
c = 91.535	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
Coot	model building
MLPHARE	phasing
PHENIX	phasing
REFMAC	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-19 
Deposition Author(s): Nocek, B., Mulligan, R., Abdullah, J., Otwinowski, Z., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-08-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary