3CJN | pdb_00003cjn

Crystal structure of transcriptional regulator, MarR family, from Silicibacter pomeroyi

• PDB DOI: https://doi.org/10.2210/pdb3CJN/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Ruegeria pomeroyi DSS-3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-13 Released: 2008-03-25 
• Deposition Author(s): Chang, C., Volkart, L., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Crystal structure of MarR family transcriptional regulator from Silicibacter pomeroyi.

Chang, C., Volkart, L., Freeman, L., Joachimiak, 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: 18.57 kDa 
• Atom Count: 1,297 
• Modeled Residue Count: 146 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, MarR family	A	162	Ruegeria pomeroyi DSS-3	Mutation(s): 0  Gene Names: SPO1458
UniProt
Find proteins for Q5LTF6 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LTF6  Go to UniProtKB:  Q5LTF6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.976	α = 90
b = 87.976	β = 90
c = 43.197	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Chang, C., Volkart, L., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary