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Atomic model of the Ocr-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.

by single particle reconstruction, at 18 A resolution

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#1: Depositted structure unit, Made by Jmol

#2: Superimposing with EM 3D map: EMDB-1534, Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2y7c
TitleAtomic model of the Ocr-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.
DescriptorTYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN (E.C.3.1.21.3)
TYPE I RESTRICTION ENZYME ECOKI M PROTEIN (E.C.3.1.21.3
2.1.1.72)
GENE 0.3 PROTEIN
KeywordsTRANSFERASE
AuthorsKennaway, C.K., Obarska-Kosinska, A., White, J.H., Tuszynska, I., Cooper, L.P., Bujnicki, J.M., Trinick, J., Dryden, D.T.F.
DateDeposition: 2011-01-31, Release: 2011-02-09
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Made by Jmol

#2: Superimposing with EM 3D map: EMDB-1534, Made by UCSF CHIMERA

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EMDB-1534

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List of similar structure data about Omokage system
Article
Citation - primary
ArticleNucleic Acids Res., Vol. 37, Issue 3, Page 762-70, Year 2009
TitleThe structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein.
AuthorsChristopher K Kennaway, Agnieszka Obarska-Kosinska, John H White, Irina Tuszynska, Laurie P Cooper, Janusz M Bujnicki, John Trinick, David T F Dryden
Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK.
KeywordsDNA (chemistry, 9007-49-2), DNA modification methylase EcoKI (2.1.1.-), Escherichia coli (enzymology), Models, Molecular, Molecular Mimicry, Ocr protein, bacteriophage T7, Site-Specific DNA-Methyltransferase (Adenine-Specific) (chemistry, 2.1.1.72), Viral Proteins (chemistry)
LinksDOI: 10.1093/nar/gkn988, PubMed: 19074193, PMC: PMC2647291
Components
ID 1 : HSDS TYPE I DNA RESTRICTION SPECIFICITY SUBUNIT, S.ECOKI, TYPE I RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN, S PROTEIN
Image
DescriptionTYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN
Typepolypeptide(L)
Formula weight51468.723 Da
Number of molecules1
ID1
Ec3.1.21.3
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI


Strain: K
LinksUniProt: P05719, Sequence view
ID 2 : HSDM TYPE I DNA RESTRICTION METHYLTRANSFERASE SUBUNIT, M.ECOKI
Image
DescriptionTYPE I RESTRICTION ENZYME ECOKI M PROTEIN
Typepolypeptide(L)
Formula weight59378.996 Da
Number of molecules2
ID2
Ec3.1.21.3, 2.1.1.72
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
Strain: K
LinksUniProt: P08957, Sequence view
ID 3 : OCR ANTIRESTRICTION PROTEIN, DNA MIMIC
Image
DescriptionGENE 0.3 PROTEIN
Typepolypeptide(L)
Formula weight13690.008 Da
Number of molecules2
ID3
SourceMethod: Isolated from a genetically manipulated source
Gene: ID:10760, ENTEROBACTERIA PHAGE T7
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P03775, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameM.ECOKI WITH OCR
Buffer
Name20MM TRIS-CL, 100 MM NACL
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeNEGATIVE STAIN
Sample preparation
pH4.7
Sample concentration0.05 mg/ml
Sample support
DetailsCARBON
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: OTHER
Date2008-02-01
Electron gun
Electron sourceTUNGSTEN HAIRPIN
Accelerating voltage80 kV
Electron dose25 e/A**2
Illumination modeMEDIUM DOSE
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 39500 X, Nominal: 40000 X
CsNominal: 2 mm
Nominal defocusMax: 870 nm, Min: 275 nm
Specimen holder
Temperature294 Kelvin
Detector
TypeKODAK SO163 FILM
Processing
2D projection selection
Number of particles17807
Software nameIMAGIC, EMAN, MRC,UROX,CHIMERA
3D reconstruction
Actual pixel size3.12 A/pix
CTF correction methodFILTERED AT FIRST ZERO
DetailsHSDM N-TERMINAL DOMAIN RETRACED FROM PDB ENTRY 2AR0. DISORDERED C-TERMINUS OF HSDM MODELLED INTO DENSITY.
Magnification calibrationTMV
Nominal pixel size3.12 A/pix
Resolution18 A
3D fitting
MethodUROX
Refinement ProtocolRIGID BODY
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
PDB entry ID1S7Z, 1YF2, 2AR0
Refine
Refine idELECTRON MICROSCOPY
Ls d res high18.00 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high18.00
Total atoms13725
Protein atoms13725
Download
PDB format
Allpdb2y7c.ent.gz
pdb2y7c.ent (uncompressed file)
Header onlypdb2y7c.ent.gz
mmCIF format
mmCIF2y7c.cif.gz
XML format
All2y7c.xml.gz
No-atom2y7c-noatom.xml.gz
Ext-atom2y7c-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.7 MB
.webm (WebM/VP8 format), 3.5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.6 MB