3B79 | pdb_00003b79

Crystal structure of the N-terminal peptidase C39 like domain of the toxin secretion ATP-binding protein from Vibrio parahaemolyticus

PDB DOI: https://doi.org/10.2210/pdb3B79/pdb

Classification: NUCLEOTIDE BINDING PROTEIN
Organism(s): Vibrio parahaemolyticus RIMD 2210633
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-10-30 Released: 2007-11-13
Deposition Author(s): Kim, Y., Li, H., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free:
0.182 (Depositor), 0.178 (DCC)
R-Value Work:
0.155 (Depositor), 0.151 (DCC)
R-Value Observed:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the N-terminal peptidase C39 like domain of the toxin secretion ATP-binding protein from Vibrio parahaemolyticus.

Kim, Y., Li, H., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 14.34 kDa
Atom Count: 1,327
Modeled Residue Count: 125
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin secretion ATP-binding protein	A	129	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0 Gene Names: VPA1736
UniProt
Find proteins for Q87FE3 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87FE3 Go to UniProtKB: Q87FE3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q87FE3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free: 0.182 (Depositor), 0.178 (DCC)
R-Value Work: 0.155 (Depositor), 0.151 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.173	α = 90
b = 46.173	β = 90
c = 105.975	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
MLPHARE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-11-13

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-11-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

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.