3HIM | pdb_00003him

The Crystal Structure of a Bacterial Regulatory Protein in the tetR Family from Rhodococcus RHA1 to 2.2A

• PDB DOI: https://doi.org/10.2210/pdb3HIM/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Rhodococcus jostii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-20 Released: 2009-05-26 
• Deposition Author(s): Stein, A.J., Binkowski, T.A., Evdokimova, E., Kagan, O., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.248 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

The Crystal Structure of a Bacterial Regulatory Protein in the tetR Family from Rhodococcus RHA1 to 2.2A

Stein, A.J., Binkowski, T.A., Evdokimova, E., Kagan, O., Edwards, A., Savchenko, A., Joachimiak, A.

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: 45.36 kDa 
• Atom Count: 2,977 
• Modeled Residue Count: 382 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcriptional regulator	A, B	211	Rhodococcus jostii	Mutation(s): 0
UniProt
Find proteins for Q0SD48 (Rhodococcus jostii (strain RHA1)) Explore Q0SD48  Go to UniProtKB:  Q0SD48

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.248 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.053	α = 90
b = 63.042	β = 90
c = 94.766	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	phasing
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Stein, A.J., Binkowski, T.A., Evdokimova, E., Kagan, O., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references