2RDP | pdb_00002rdp

The structure of a MarR family protein from Bacillus stearothermophilus

• PDB DOI: https://doi.org/10.2210/pdb2RDP/pdb

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


• Deposited: 2007-09-24 Released: 2007-11-13 
• Deposition Author(s): Cuff, M.E., Duggan, E., Dementieva, I., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.253 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

The structure of a MarR family protein from Bacillus stearothermophilus.

Cuff, M.E., Duggan, E., Dementieva, I., Moy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.17 kDa 
• Atom Count: 1,283 
• Modeled Residue Count: 140 
• Deposited Residue Count: 150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative transcriptional regulator MarR	A	150	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: RBSTP1228
UniProt
Find proteins for D0VWY6 (Geobacillus stearothermophilus) Explore D0VWY6  Go to UniProtKB:  D0VWY6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
BME	E [auth A], F [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.253 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.643	α = 90
b = 73.643	β = 90
c = 90.432	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Cuff, M.E., Duggan, E., Dementieva, I., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary