2O0Y

Crystal structure of putative transcriptional regulator RHA1_ro06953 (IclR-family) from Rhodococcus sp.

• PDB DOI: https://doi.org/10.2210/pdb2O0Y/pdb

• Classification: TRANSCRIPTION
• Organism(s): Rhodococcus sp. (in: high G+C Gram-positive bacteria)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-11-28 Released: 2006-12-26 
• Deposition Author(s): Chruszcz, M., Wang, S., Skarina, T., Onopriyenko, O., Cymborowski, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

Literature

Crystal Structure of Putative Transcriptional Regul 2 Rha1_Ro06953(Iclr-Family) from Rhodococcus Sp.

Chruszcz, M., Wang, S., Skarina, T., Onopriyenko, O., Cymborowski, M., Savchenko, A., Edwards, A., Minor, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
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 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.78 kDa 
• Atom Count: 7,907 
• Modelled Residue Count: 994 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A, B, C, D	260	Rhodococcus sp. (in: high G+C Gram-positive bacteria)	Mutation(s): 3  Gene Names: RHA00472
UniProt
Find proteins for Q0S167 (Rhodococcus jostii (strain RHA1)) Explore Q0S167  Go to UniProtKB:  Q0S167

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.247	α = 74.88
b = 69.027	β = 71.47
c = 79.214	γ = 68.87

Software Package:

Software Name	Purpose
HKL-3000	phasing
RESOLVE	model building
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHELXE	model building
DM	phasing
MLPHARE	phasing
RESOLVE	phasing
ARP/wARP	model building
O	model building
Coot	model building
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-26 
Deposition Author(s): Chruszcz, M., Wang, S., Skarina, T., Onopriyenko, O., Cymborowski, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-12-26
  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: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection