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)

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)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of cppA protein from Streptococcus pneumoniae TIGR4

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

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X4I9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

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

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

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Entry History

Deposition Data

Released Date: 2008-08-19

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.