3ON2 | pdb_00003on2

Structure of a protein with unknown function from Rhodococcus sp. RHA1

• PDB DOI: https://doi.org/10.2210/pdb3ON2/pdb

• Classification: structural genomics, unknown function
• Organism(s): Rhodococcus jostii RHA1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-27 Released: 2010-09-22 
• Deposition Author(s): Fan, Y., Evdokimova, E., Egorova, O., Savchenko, A., Joachimiak, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.222 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Structure of a protein with unknown function from Rhodococcus sp. RHA1

Fan, Y., Evdokimova, E., Egorova, O., Savchenko, A., Joachimiak, A., Edwards, 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 85.81 kDa 
• Atom Count: 7,070 
• Modeled Residue Count: 774 
• Deposited Residue Count: 796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcriptional regulator	A, B, C, D	199	Rhodococcus jostii RHA1	Mutation(s): 0  Gene Names: RHA1_ro01040
UniProt
Find proteins for Q0SHW9 (Rhodococcus jostii (strain RHA1)) Explore Q0SHW9  Go to UniProtKB:  Q0SHW9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG6	G [auth A], J [auth B], L [auth C], N [auth D]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C12 H26 O6 DMDPGPKXQDIQQG-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], M [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 1.96 Å
• R-Value Free:  0.222 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.889	α = 90
b = 86.863	β = 95.51
c = 115.255	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Fan, Y., Evdokimova, E., Egorova, O., Savchenko, A., Joachimiak, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-22
  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: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary