3BRO | pdb_00003bro

Crystal structure of the transcription regulator MarR from Oenococcus oeni PSU-1

• PDB DOI: https://doi.org/10.2210/pdb3BRO/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Oenococcus oeni PSU-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-12-21 Released: 2008-01-15 
• Deposition Author(s): Kim, Y., Volkart, L., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.247 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Crystal Structure of the Transcription Regulator MarR from Oenococcus oeni PSU-1.

Kim, Y., Volkart, L., Gu, M., 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 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.88 kDa 
• Atom Count: 5,326 
• Modeled Residue Count: 544 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A, B, C, D	141	Oenococcus oeni PSU-1	Mutation(s): 0  Gene Names: OEOE_1854
UniProt
Find proteins for Q04CY6 (Oenococcus oeni (strain ATCC BAA-331 / PSU-1)) Explore Q04CY6  Go to UniProtKB:  Q04CY6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.247 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.489	α = 90
b = 80.426	β = 90
c = 143.257	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
MLPHARE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-15 
Deposition Author(s): Kim, Y., Volkart, L., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-01-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary