3V4G | pdb_00003v4g

1.60 Angstrom resolution crystal structure of an arginine repressor from Vibrio vulnificus CMCP6

• PDB DOI: https://doi.org/10.2210/pdb3V4G/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Vibrio vulnificus YJ016
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-12-14 Released: 2012-01-04 
• Deposition Author(s): Halavaty, A.S., Minasov, G., Filippova, E., Shuvalova, L., Winsor, J., Dubrovska, I., Peterson, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.198 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Models: experimental

Literature

1.60 Angstrom resolution crystal structure of an arginine repressor from Vibrio vulnificus CMCP6

Halavaty, A.S., Minasov, G., Filippova, E., Shuvalova, L., Winsor, J., Dubrovska, I., Peterson, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 19.91 kDa 
• Atom Count: 1,441 
• Modeled Residue Count: 145 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginine repressor	A	180	Vibrio vulnificus YJ016	Mutation(s): 0  Gene Names: argR, VV0466
UniProt
Find proteins for Q7MP98 (Vibrio vulnificus (strain YJ016)) Explore Q7MP98  Go to UniProtKB:  Q7MP98

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.198 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33v4g

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.308	α = 90
b = 73.308	β = 90
c = 118.597	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-04 
Deposition Author(s): Halavaty, A.S., Minasov, G., Filippova, E., Shuvalova, L., Winsor, J., Dubrovska, I., Peterson, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-01-04
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description