3ER6

Crystal structure of a putative transcriptional regulator protein from Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb3ER6/pdb

• Classification: structural genomics, unknown function
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-10-01 Released: 2008-10-14 
• Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Chang, S., Ozyurt, S., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.231 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of a putative transcriptional regulator protein from Vibrio parahaemolyticus

Bonanno, J.B., Freeman, J., Bain, K.T., Chang, S., Ozyurt, S., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 139.97 kDa 
• Atom Count: 9,362 
• Modelled Residue Count: 1,133 
• Deposited Residue Count: 1,254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator protein	A, B, C, D, E, F	209	Vibrio parahaemolyticus	Mutation(s): 1  Gene Names: VPA0716
UniProt
Find proteins for Q87I90 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87I90  Go to UniProtKB:  Q87I90

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.231 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.268	α = 90
b = 105.268	β = 90
c = 101.745	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-14 
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Chang, S., Ozyurt, S., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-10-14
  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: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references
• Version 1.6: 2023-12-27
  Changes: Data collection