Macromolecule Content

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

4GD5

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

PDB DOI: 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.186
R-Value Work: 0.150
R-Value Observed: 0.152

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2YSI2
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B]	D [auth A], E [auth A], H [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.150
R-Value Observed: 0.152
Space Group: P 1 2₁ 1
Diffraction Data DOI: 10.18430/M34GD5

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-08-15

Deposition Author(s):

Brunzelle, J.S.

Onopriyenko, O.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-08-15
Type: Initial release
Version 1.1: 2013-03-20
Changes: Other

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.