3NTS | pdb_00003nts

Catalytic domain of VsdC from Aeromonas hydrophila

PDB DOI: https://doi.org/10.2210/pdb3NTS/pdb

Classification: TRANSFERASE
Organism(s): Aeromonas hydrophila
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-05 Released: 2011-06-22
Deposition Author(s): Pfoh, R., Shniffer, A., Merrill, A.R., Pai, E.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.291 (Depositor), 0.280 (DCC)
R-Value Work:
0.271 (Depositor), 0.270 (DCC)
R-Value Observed:
0.272 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Biochemical characterization of an actin-targeting ADP ribosyltransferase from aeromonas hydrophila and the identification of a novel inhibitor for this toxin family

Shniffer, A., Suarez, G., Turgeon, Z.J., Pfoh, R., Fieldhouse, R.J., K Chopra, A., Pai, E.F., Merrill, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 53.41 kDa
Atom Count: 2,854
Modelled Residue Count: 374
Deposited Residue Count: 482
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VsdC	A, B	241	Aeromonas hydrophila	Mutation(s): 0 Gene Names: vsdC
UniProt
Find proteins for Q49TP5 (Aeromonas hydrophila) Explore Q49TP5 Go to UniProtKB: Q49TP5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q49TP5
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.291 (Depositor), 0.280 (DCC)
R-Value Work: 0.271 (Depositor), 0.270 (DCC)
R-Value Observed: 0.272 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.8	α = 90
b = 87.8	β = 90
c = 295.7	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
SADABS	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Derived calculations

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.