5B7H | pdb_00005b7h

OxyR2 regulatory domain C206S mutant from Vibrio vulnificus

• PDB DOI: https://doi.org/10.2210/pdb5B7H/pdb

• Classification: TRANSCRIPTION
• Organism(s): Vibrio vulnificus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-06-07 Released: 2017-06-07 
• Deposition Author(s): Jo, I., Ha, N.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Structural basis for hypersensitivity of OxyR2 from Vibrio vulnificus

Jo, I., Ha, N.-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)

Macromolecule Content 

• Total Structure Weight: 48.55 kDa 
• Atom Count: 4,076 
• Modeled Residue Count: 425 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysR family transcriptional regulator	A, B	219	Vibrio vulnificus	Mutation(s): 1
UniProt
Find proteins for A0A087I947 (Vibrio vulnificus) Explore A0A087I947  Go to UniProtKB:  A0A087I947

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.703	α = 90
b = 137.58	β = 90
c = 96.914	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Jo, I., Ha, N.-C.

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description