2ZB9 | pdb_00002zb9

Crystal structure of TetR family transcription regulator SCO0332

• PDB DOI: https://doi.org/10.2210/pdb2ZB9/pdb

• Classification: TRANSCRIPTION
• Organism(s): Streptomyces coelicolor
• Expression System: Rhodococcus erythropolis
• Mutation(s): No 


• Deposited: 2007-10-16 Released: 2008-01-29 
• Deposition Author(s): Okada, U., Kondo, K., Watanabe, N., Yao, M., Tanaka, I.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.196 (DCC) 

Literature

Structural and functional analysis of the TetR-family transcriptional regulator SCO0332 from Streptomyces coelicolor

Okada, U., Kondo, K., Hayashi, T., Watanabe, N., Yao, M., Tamura, T., Tanaka, I.

(2008) Acta Crystallogr D Biol Crystallogr 64: 198-205

• PubMed: 18219120 
• DOI: https://doi.org/10.1107/S0907444907059835
• Primary Citation Related Structures: 
  2ZB9


• PubMed Abstract: 
  

  SCO0332 protein is a putative TetR-family transcriptional regulator from Streptomyces coelicolor A3(2). The crystal structure of SCO0332 was determined at 2.25 A resolution by single-wavelength anomalous diffraction (SAD) phasing using the S atoms of the native protein. SCO0332 contains a helix-turn-helix (HTH) DNA-binding motif in its N-terminal region and forms a homodimer. The overall structure of SCO0332 shows significant similarity to other TetR-family regulators. A systematic evolution of ligands by exponential enrichment (SELEX) analysis indicated that SCO0332 has sequence-specific DNA-binding ability and determined the position of the operator element of SCO0332 on the chromosomal DNA of S. coelicolor. An electrophoretic mobility-shift assay (EMSA) showed that SCO0332 binds to the operator sequence upstream of the sco0330 gene, which encodes a putative short-chain oxidoreductase. These results suggest that SCO0332 is a transcriptional repressor that regulates sco0330 gene expression.

---

Organizational Affiliation: 
• Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.

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: 47.26 kDa 
• Atom Count: 3,123 
• Modeled Residue Count: 370 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator	A, B	214	Streptomyces coelicolor	Mutation(s): 0  Gene Names: sco0332
UniProt
Find proteins for Q9RK47 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9RK47  Go to UniProtKB:  Q9RK47

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.196 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.413	α = 90
b = 77.778	β = 104.31
c = 57.272	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
SHELXS	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-29 
Deposition Author(s): Okada, U., Kondo, K., Watanabe, N., Yao, M., Tanaka, I.

Revision History  

• Version 1.0: 2008-01-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references