3D6W | pdb_00003d6w

LytTr DNA-binding domain of putative methyl-accepting/DNA response regulator from Bacillus cereus.

• PDB DOI: https://doi.org/10.2210/pdb3D6W/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Bacillus cereus ATCC 10987
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-20 Released: 2008-07-15 
• Deposition Author(s): Osipiuk, J., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.209 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

X-ray crystal structure of LytTr DNA-binding domain of putative methyl-accepting/DNA response regulator from Bacillus cereus.

OSIPIUK, J., EVDOKIMOVA, E., KUDRITSKA, M., SAVCHENKO, A., EDWARDS, A.M., JOACHIMIAK, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.88 kDa 
• Atom Count: 1,866 
• Modeled Residue Count: 218 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-accepting/DNA response regulator	A, B	111	Bacillus cereus ATCC 10987	Mutation(s): 0  Gene Names: BCE_1947
UniProt
Find proteins for Q73A38 (Bacillus cereus (strain ATCC 10987 / NRS 248)) Explore Q73A38  Go to UniProtKB:  Q73A38

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	E [auth A], G [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.40 Å
• R-Value Free:  0.209 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.784	α = 90
b = 88.784	β = 90
c = 74.425	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Osipiuk, J., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary