2P7J | pdb_00002p7j

Crystal structure of the domain of putative sensory box/GGDEF family protein from Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb2P7J/pdb

• Classification: TRANSCRIPTION
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2007-03-20 Released: 2007-05-01 
• Deposition Author(s): Wu, R., James, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.239 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

The crystal structure of the domain of putative sensory box/GGDEF family protein from Vibrio parahaemolyticus

Wu, R., James, A., 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.

Macromolecule Content 

• Total Structure Weight: 66.89 kDa 
• Atom Count: 4,836 
• Modeled Residue Count: 539 
• Deposited Residue Count: 574 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sensory box/GGDEF family protein	A, B	287	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 3  Gene Names: VP0354 EC: 2.7.7.65
UniProt
Find proteins for Q87SR8 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87SR8  Go to UniProtKB:  Q87SR8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	F [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
NA	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.239 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.98	α = 90
b = 81.596	β = 90
c = 121.851	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-01 
Deposition Author(s): Wu, R., James, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-05-01
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary