4GD5 | pdb_00004gd5

X-ray Crystal Structure of a Putative Phosphate ABC Transporter Substrate-Binding Protein with Bound Phosphate from Clostridium perfringens

• PDB DOI: https://doi.org/10.2210/pdb4GD5/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Clostridium perfringens ATCC 13124
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-07-31 Released: 2012-08-15 
• Deposition Author(s): Brunzelle, J.S., Wawrzak, Z., Onopriyenko, O., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.186 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

X-ray Crystal Structure of a Putative Phosphate ABC Transporter Substrate-Binding Protein with Bound Phosphate from Clostridium perfringens

Brunzelle, J.S., Wawrzak, Z., Onopriyenko, O., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and 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)

Macromolecule Content 

• Total Structure Weight: 60.5 kDa 
• Atom Count: 4,474 
• Modeled Residue Count: 486 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphate ABC transporter, phosphate-binding protein	A, B	279	Clostridium perfringens ATCC 13124	Mutation(s): 0  Gene Names: CPF_0617, pstS
UniProt
Find proteins for A0A0H2YSI2 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YSI2  Go to UniProtKB:  A0A0H2YSI2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	I [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	C [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A], E [auth A], H [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.186 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34GD5

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.888	α = 90
b = 73.302	β = 102.09
c = 56.415	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
PHENIX	model building
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Brunzelle, J.S., Wawrzak, Z., Onopriyenko, O., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2013-03-20
  Changes: Other
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary