1YLF | pdb_00001ylf

X-ray crystal structure of BC1842 protein from Bacillus cereus, a member of the Rrf2 family of putative transcription regulators.

• PDB DOI: https://doi.org/10.2210/pdb1YLF/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Bacillus cereus ATCC 14579
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-01-19 Released: 2005-02-01 
• Deposition Author(s): Osipiuk, J., Wu, R., Moy, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.250 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

X-ray crystal structure of BC1842 protein from Bacillus cereus, a member of the Rrf2 family of putative transcription regulators.

Osipiuk, J., Wu, R., Moy, S., Collart, F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PQS (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 generated by PQS (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 50.78 kDa 
• Atom Count: 2,768 
• Modeled Residue Count: 354 
• Deposited Residue Count: 447 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RRF2 family protein	A, B, C	149	Bacillus cereus ATCC 14579	Mutation(s): 7  Gene Names: BC1842
UniProt
Find proteins for Q81EX1 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81EX1  Go to UniProtKB:  Q81EX1

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.250 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.08	α = 90
b = 73.08	β = 90
c = 157.68	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	phasing
CNS	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-01 
Deposition Author(s): Osipiuk, J., Wu, R., Moy, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-02-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary