3LET | pdb_00003let

Crystal Structure of Fic domain containing AMPylator, VopS

PDB DOI: https://doi.org/10.2210/pdb3LET/pdb

Classification: TRANSFERASE
Organism(s): Vibrio parahaemolyticus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-01-15 Released: 2010-04-21
Deposition Author(s): Luong, P.H., Kinch, L.N., Brautigam, C.A., Grishin, N.V., Tomchick, D.R., Orth, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.224 (Depositor), 0.175 (DCC)
R-Value Work:
0.175 (Depositor), 0.176 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

Structural and Kinetic Analysis of VopS with Fic Domain Supports a Direct Transfer Mechanism for AMPylation

Luong, P.H., Kinch, L.N., Brautigam, C.A., Grishin, N.V., Tomchick, D.R., Orth, K.

To be published.

Macromolecule Content

Total Structure Weight: 67.95 kDa
Atom Count: 5,156
Modeled Residue Count: 612
Deposited Residue Count: 628
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine monophosphate-protein transferase vopS	A, B	314	Vibrio parahaemolyticus	Mutation(s): 0 Gene Names: vopS, VP 1686, VP1686 EC: 2.7.7.1 (PDB Primary Data), 2.7.7.108 (UniProt)
UniProt
Find proteins for Q87P32 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87P32 Go to UniProtKB: Q87P32
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87P32
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.224 (Depositor), 0.175 (DCC)
R-Value Work: 0.175 (Depositor), 0.176 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.669	α = 90
b = 62.325	β = 91.31
c = 75.762	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
SHELXS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-04-21

Deposition Author(s):

Brautigam, C.A.

Revision History (Full details and data files)

Version 1.0: 2010-04-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2024-02-21
Changes: Data collection, Database references

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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.