3H05

The Crystal Structure of a Putative Nicotinate-nucleotide Adenylyltransferase from Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb3H05/pdb

• Classification: structural genomics, unknown function
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-08 Released: 2009-04-21 
• Deposition Author(s): Stein, A.J., Cuff, M.E., Sather, A., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.214 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

The Crystal Structure of a Putative Nicotinate-nucleotide Adenylyltransferase from Vibrio parahaemolyticus

Stein, A.J., Cuff, M.E., Sather, A., Shackelford, G., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 40.08 kDa 
• Atom Count: 2,844 
• Modelled Residue Count: 318 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein VPA0413	A, B	177	Vibrio parahaemolyticus	Mutation(s): 0
UniProt
Find proteins for Q87J40 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87J40  Go to UniProtKB:  Q87J40

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.214 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.206	α = 90
b = 70.722	β = 90
c = 130.495	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Stein, A.J., Cuff, M.E., Sather, A., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations