3G7R | pdb_00003g7r

Crystal structure of SCO4454, a TetR-family transcriptional regulator from Streptomyces coelicolor

• PDB DOI: https://doi.org/10.2210/pdb3G7R/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Streptomyces coelicolor A3(2)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-10 Released: 2009-03-10 
• Deposition Author(s): Singer, A.U., Xu, X., Chang, C., Gu, J., Edwards, A.M., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.174 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

Structure and ligand specificity of SCO4454, a TetR-family transcriptional regulator from Streptomyces coelicolor

Singer, A.U., Xu, X., Chang, C., Edwards, A.M., Joachimiak, A., Savchenko, 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: 50.33 kDa 
• Atom Count: 3,973 
• Modeled Residue Count: 391 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator	A, B	221	Streptomyces coelicolor A3(2)	Mutation(s): 0  Gene Names: SCD6.32c, SCO4454
UniProt
Find proteins for Q9KZX2 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9KZX2  Go to UniProtKB:  Q9KZX2

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	LA [auth B], MA [auth B], T [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
PEG	GA [auth B], R [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	HA [auth B], IA [auth B], KA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	JA [auth B], S [auth A]	SODIUM ION Na FKNQFGJONOIPTF-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: 1.38 Å
• R-Value Free:  0.174 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.103	α = 90
b = 59.129	β = 101.38
c = 66.895	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Singer, A.U., Xu, X., Chang, C., Gu, J., Edwards, A.M., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary