- PDB-2ar0: Crystal structure of Type I restriction enzyme EcoKI M protein (E... -
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Basic information
Entry
Database: PDB / ID: 2ar0
Title
Crystal structure of Type I restriction enzyme EcoKI M protein (EC 2.1.1.72) (M.EcoKI)
Components
Type I restriction enzyme EcoKI M protein
Keywords
TRANSCRIPTION / TRANSFERASE / Structural Genomics / Protein Structure Initiative / NYSGXRC / T824 / Q9PNP0 Restriction modification enzyme / Type I restriction enzyme EcoKI M protein / methyltransferase / PSI / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information
type I site-specific deoxyribonuclease complex / N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / DNA binding / cytosol Similarity search - Function
N6 adenine-specific DNA methyltransferase, N-terminal domain / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / HsdM N-terminal domain / N-6 DNA Methylase / DNA methylase, adenine-specific / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Ferritin / Vaccinia Virus protein VP39 ...N6 adenine-specific DNA methyltransferase, N-terminal domain / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / HsdM N-terminal domain / N-6 DNA Methylase / DNA methylase, adenine-specific / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Ferritin / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Type: MARRESEARCH / Detector: CCD / Date: Mar 17, 2004 / Details: Focussing mirrors down stream of monochromator
Radiation
Monochromator: FLAT DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.975 Å / Relative weight: 1
Reflection
Resolution: 2.8→30 Å / Num. all: 70488 / Num. obs: 70488 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 2.22 % / Biso Wilson estimate: 35 Å2 / Rsym value: 0.113 / Net I/σ(I): 8.6
Reflection shell
Resolution: 2.8→2.9 Å / Num. unique all: 7016 / Rsym value: 0.551 / % possible all: 95.7
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Processing
Software
Name
Version
Classification
DENZO
datareduction
SCALEPACK
datascaling
SOLVE
phasing
CNS
1.1
refinement
Refinement
Method to determine structure: SAD / Resolution: 2.8→19.81 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 168223.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: See REMARK 400 for details on un-observed residues in electron density map
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