2ZDS

Crystal Structure of SCO6571 from Streptomyces coelicolor A3(2)

• PDB DOI: https://doi.org/10.2210/pdb2ZDS/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Streptomyces coelicolor
• Expression System: Rhodococcus erythropolis
• Mutation(s): No 


• Deposited: 2007-11-27 Released: 2008-12-02 
• Deposition Author(s): Begum, P., Gao, Y.G., Sakai, N., Yao, M., Watanabe, N., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.210 
• R-Value Work: 0.167 
• R-Value Observed: 0.167 

Literature

Crystal structure of SCO6571 from Streptomyces coelicolor A3(2).

Begum, P., Sakai, N., Hayashi, T., Gao, Y.G., Tamura, T., Watanabe, N., Yao, M., Tanaka, I.

(2008) Protein Pept Lett 15: 709-712

• PubMed: 18782066 
• DOI: https://doi.org/10.2174/092986608785133636
• Primary Citation of Related Structures:  
  2ZDS


• PubMed Abstract: 
  

  SCO6571 protein from Streptomyces coelicolor A3(2) was overexpressed and purified using Rhodococcus erythropolis as an expressing host. Crystals of selenomethionine-substituted SCO6571 have been obtained by vapor diffusion method. SCO6571 crystals diffract to 2.3 A and were found to belong to the orthorhombic space group P2(1)2(1)2(1) with unit cell parameters a = 84.5, b = 171.6, c = 184.8 A. Six molecules in the asymmetric unit give a crystal volume per protein mass (V(M)) of 2.97 A (3) Da(-1) and solvent content of 58.6 %. The structure was solved by the single wavelength anomalous diffraction (SAD) method. SCO6571 is a TIM-barrel fold protein that assembles into a hexameric molecule with D(3) symmetry.

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Organizational Affiliation: 

Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 233.81 kDa 
• Atom Count: 16,757 
• Modelled Residue Count: 1,930 
• Deposited Residue Count: 2,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative DNA-binding protein	A, B, C, D, E, F	340	Streptomyces coelicolor	Mutation(s): 0  Gene Names: sco6571
UniProt
Find proteins for O69946 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore O69946  Go to UniProtKB:  O69946

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.210 
• R-Value Work: 0.167 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.481	α = 90
b = 171.593	β = 90
c = 184.796	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-02 
Deposition Author(s): Begum, P., Gao, Y.G., Sakai, N., Yao, M., Watanabe, N., Tanaka, I.

Revision History  

• Version 1.0: 2008-12-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2019-10-16
  Changes: Data collection, Database references, Derived calculations