3CDH | pdb_00003cdh

Crystal structure of the MarR family transcriptional regulator SPO1453 from Silicibacter pomeroyi DSS-3

• PDB DOI: https://doi.org/10.2210/pdb3CDH/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Ruegeria pomeroyi DSS-3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-02-26 Released: 2008-03-18 
• Deposition Author(s): Kim, Y., Volkart, L., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 
  0.227 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Crystal structure of the MarR family transcriptional regulator SPO1453 from Silicibacter pomeroyi.

Kim, Y., Volkart, L., Keigher, 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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.11 kDa 
• Atom Count: 2,499 
• Modeled Residue Count: 270 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, MarR family	A, B	155	Ruegeria pomeroyi DSS-3	Mutation(s): 0  Gene Names: SPO1453
UniProt
Find proteins for Q5LTG1 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LTG1  Go to UniProtKB:  Q5LTG1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.69 Å
• R-Value Free:  0.227 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.14	α = 90
b = 124.14	β = 90
c = 140.186	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
Coot	model building
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Kim, Y., Volkart, L., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary