3BO6 | pdb_00003bo6

Structure of the Chromobacterium violaceum VirA (SpvC) Phosphothreonine Lyase effector protein

PDB DOI: https://doi.org/10.2210/pdb3BO6/pdb

Classification: LYASE
Organism(s): Chromobacterium violaceum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-12-17 Released: 2008-11-25
Deposition Author(s): Brennan, D.F., Roe, S.M., Barford, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.189 (Depositor), 0.188 (DCC)
R-Value Work:
0.159 (Depositor), 0.158 (DCC)
R-Value Observed:
0.160 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3BO6

This is version 1.3 of the entry. See complete history.

Literature

Structure and Mechanism of the Chromobacterium violaceum VirA Phosphothreonine Lyase Type III Secretion System Effector

Brennan, D.F., Roe, S.M., Barford, D.

To be published.

Macromolecule Content

Total Structure Weight: 50.57 kDa
Atom Count: 4,304
Modeled Residue Count: 435
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrophilic protein, virA protein	A, B	220	Chromobacterium violaceum	Mutation(s): 0 Gene Names: spvC EC: 4.2.3
UniProt
Find proteins for Q7NYG6 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NYG6 Go to UniProtKB: Q7NYG6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7NYG6
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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.189 (Depositor), 0.188 (DCC)
R-Value Work: 0.159 (Depositor), 0.158 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.671	α = 90
b = 119.777	β = 105.63
c = 44.492	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
SHELX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
SHELXCD	phasing
SHELXE	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-11-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-11-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-03-13
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.