4B8X | pdb_00004b8x

Near atomic resolution crystal structure of Sco5413, a MarR family transcriptional regulator from Streptomyces coelicolor

• PDB DOI: https://doi.org/10.2210/pdb4B8X/pdb

• Classification: TRANSCRIPTION
• Organism(s): Streptomyces coelicolor
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-31 Released: 2012-10-17 
• Deposition Author(s): Holley, T.A., Stevenson, C.E.M., Bibb, M.J., Lawson, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Literature

High Resolution Crystal Structure of Sco5413, a Widespread Actinomycete Marr Family Transcriptional Regulator of Unknown Function.

Holley, T.A., Stevenson, C.E.M., Bibb, M.J., Lawson, D.M.

(2013) Proteins 81: 176

• PubMed: 23042442 
• DOI: https://doi.org/10.1002/prot.24197
• Primary Citation Related Structures: 
  4B8X


• PubMed Abstract: 
  

  The crystal structure of Sco5413 from Streptomyces coelicolor A3(2) has been determined at 1.25 Å resolution, the highest resolution reported for a MarR family transcriptional regulator. Putative orthologs are encoded by the majority of sequenced actinomycete genomes, and may play roles in regulating growth and antibiotic production, but they have yet to be assigned a precise function. Sco5413 forms a homodimer and, through comparisons with other MarR family protein structures, we postulate that it adopts a conformation compatible with DNA binding, and that a channel at the dimer interface, lined by well-conserved residues, is the binding site of an unidentified effector ligand.

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Organizational Affiliation: 
• Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.

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: 31.86 kDa 
• Atom Count: 2,660 
• Modeled Residue Count: 279 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POSSIBLE MARR-TRANSCRIPTIONAL REGULATOR	A, B	147	Streptomyces coelicolor	Mutation(s): 0
UniProt
Find proteins for Q9L2A7 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9L2A7  Go to UniProtKB:  Q9L2A7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.4	α = 90
b = 65.65	β = 90
c = 69.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-17 
Deposition Author(s): Holley, T.A., Stevenson, C.E.M., Bibb, M.J., Lawson, D.M.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2013-01-16
  Changes: Database references
• Version 1.2: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.3: 2019-05-22
  Changes: Data collection, Experimental preparation
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary