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)
R-Value Work:
0.271 (Depositor)
R-Value Observed:
0.272 (Depositor)

wwPDB Validation 3D Report Full Report

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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
Modeled Residue Count: 374
Deposited Residue Count: 482
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q49TP5
Sequence Annotations Expand
Reference Sequence

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)
R-Value Work: 0.271 (Depositor)
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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.