2IBD | pdb_00002ibd

Crystal structure of Probable transcriptional regulatory protein RHA5900

• PDB DOI: https://doi.org/10.2210/pdb2IBD/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Rhodococcus jostii RHA1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-09-11 Released: 2006-10-10 
• Deposition Author(s): Chang, C., Evdokimova, E., Kagan, O., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.201 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.168 (Depositor) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of Probable transcriptional regulatory protein RHA5900

Chang, C., Evdokimova, E., Kagan, O., Savchenko, A., Edwards, A.M., 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: 45.46 kDa 
• Atom Count: 3,585 
• Modeled Residue Count: 380 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Possible transcriptional regulator	A, B	204	Rhodococcus jostii RHA1	Mutation(s): 3  Gene Names: RHA1_ro04598
UniProt
Find proteins for Q0S7V2 (Rhodococcus jostii (strain RHA1)) Explore Q0S7V2  Go to UniProtKB:  Q0S7V2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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: 1.50 Å
• R-Value Free:  0.201 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.168 (Depositor) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.588	α = 90
b = 118.778	β = 90
c = 97.173	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-10 
Deposition Author(s): Chang, C., Evdokimova, E., Kagan, O., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-10-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary