5J7R | pdb_00005j7r

2.5 Angstrom Crystal Structure of Putative Lipoprotein from Clostridium perfringens

• PDB DOI: https://doi.org/10.2210/pdb5J7R/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Clostridium perfringens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-06 Released: 2016-04-20 
• Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Flores, K., Shatsman, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.268 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

2.5 Angstrom Crystal Structure of Putative Lipoprotein from Clostridium perfringens

Minasov, G., Shuvalova, L., Kiryukhina, O., Flores, K., Shatsman, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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 4-mer - A4 

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

Biological Assembly 4  

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

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

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.18 kDa 
• Atom Count: 4,566 
• Modeled Residue Count: 581 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Lipoprotein	A, B, C, D	164	Clostridium perfringens	Mutation(s): 0  Gene Names: FORC3_2834

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.268 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35j7r

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.212	α = 90
b = 118.212	β = 90
c = 71.836	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Flores, K., Shatsman, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2016-05-04
  Changes: Data collection
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary