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.

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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) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

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

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

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

Entry History 

Deposition Data

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

Revision History  

• 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