3OIO | pdb_00003oio

Crystal structure of transcriptional regulator (AraC-type DNA-binding domain-containing proteins) from Chromobacterium violaceum

• PDB DOI: https://doi.org/10.2210/pdb3OIO/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Chromobacterium violaceum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-19 Released: 2010-09-08 
• Deposition Author(s): Chang, C., Mack, J., Feldman, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Literature

Crystal structure of transcriptional regulator (AraC-type DNA-binding domain-containing proteins) from Chromobacterium violaceum

Chang, C., Mack, J., Feldman, B., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 12.97 kDa 
• Atom Count: 1,180 
• Modelled Residue Count: 112 
• Deposited Residue Count: 113 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator (AraC-type DNA-binding domain-containing proteins)	A	113	Chromobacterium violaceum	Mutation(s): 0  Gene Names: argR, CV_3088
UniProt
Find proteins for Q7NTG7 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NTG7  Go to UniProtKB:  Q7NTG7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.753	α = 90
b = 96.753	β = 90
c = 33.312	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Chang, C., Mack, J., Feldman, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-12-18
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary