2OFY | pdb_00002ofy

Crystal structure of putative XRE-family transcriptional regulator from Rhodococcus sp.

• PDB DOI: https://doi.org/10.2210/pdb2OFY/pdb

• Classification: TRANSCRIPTION
• Organism(s): Rhodococcus jostii RHA1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-01-04 Released: 2007-01-16 
• Deposition Author(s): Shumilin, I.A., Skarina, T., Onopriyenko, O., Yim, V., Chruszcz, M., 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: 1.70 Å
• R-Value Free: 
  0.239 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Crystal structure of putative XRE-family transcriptional regulator from Rhodococcus sp.

Shumilin, I.A., Skarina, T., Onopriyenko, O., Yim, V., Chruszcz, M., Cymborowski, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W.

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)

Macromolecule Content 

• Total Structure Weight: 18.63 kDa 
• Atom Count: 1,471 
• Modeled Residue Count: 162 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative XRE-family transcriptional regulator	A, B	86	Rhodococcus jostii RHA1	Mutation(s): 3  Gene Names: RHA1_ro04071
UniProt
Find proteins for Q0S9B8 (Rhodococcus jostii (strain RHA1)) Explore Q0S9B8  Go to UniProtKB:  Q0S9B8

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.239 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.54	α = 90
b = 46.073	β = 90
c = 81.842	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-16 
Deposition Author(s): Shumilin, I.A., Skarina, T., Onopriyenko, O., Yim, V., Chruszcz, M., Cymborowski, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-01-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection
• Version 1.5: 2024-11-06
  Changes: Structure summary