2ID3 | pdb_00002id3

Crystal structure of transcriptional regulator SCO5951 from Streptomyces coelicolor A3(2)

• PDB DOI: https://doi.org/10.2210/pdb2ID3/pdb

• Classification: TRANSCRIPTION
• Organism(s): Streptomyces coelicolor
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-09-14 Released: 2006-10-17 
• Deposition Author(s): Grabowski, M., Chruszcz, M., Koclega, K.D., Cymborowski, M., Gu, J., Xu, X., 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: 
  0.199 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.38 kDa 
• Atom Count: 3,359 
• Modeled Residue Count: 381 
• Deposited Residue Count: 450 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator	A, B	225	Streptomyces coelicolor	Mutation(s): 0  Gene Names: SCO5951
UniProt
Find proteins for O54180 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore O54180  Go to UniProtKB:  O54180

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A], G [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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:  0.199 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.069	α = 90
b = 85.617	β = 90
c = 126.341	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-17 
Deposition Author(s): Grabowski, M., Chruszcz, M., Koclega, K.D., Cymborowski, M., Gu, J., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-10-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: 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