Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - PDB-2y7c: Atomic model of the Ocr-bound methylase complex from the Type I r... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: PDB / ID: 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
    Specimen sourceENTEROBACTERIA PHAGE T7 / virus
    Escherichia coli / bacteria /
    MethodElectron microscopy (18 A resolution / Single particle / Negative stain)
    AuthorsKennaway, C.K. / Obarska-Kosinska, A. / White, J.H. / Tuszynska, I. / Cooper, L.P. / Bujnicki, J.M. / Trinick, J. / Dryden, D.T.F.
    CitationNucleic Acids Res., 2009, 37, 762-770

    Nucleic Acids Res., 2009, 37, 762-770 StrPapers
    The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein.
    Christopher K Kennaway / Agnieszka Obarska-Kosinska / John H White / Irina Tuszynska / Laurie P Cooper / Janusz M Bujnicki / John Trinick / David T F Dryden

    DateDeposition: Jan 31, 2011 / Release: Feb 9, 2011 / Last modification: Mar 20, 2013

    -
    Structure visualization

    Movie
    • Deposited structure unit
    • Imaged by Jmol
    • Download
    3D viewer /

    View / / Stereo:
    Center
    Zoom
    Scale
    slabnear <=> far

    fix: /
    Orientation
    Orientation Rotation
    misc. /
    Show/hide

    Downloads & links

    -
    Assembly

    Deposited unit
    A: TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN
    B: TYPE I RESTRICTION ENZYME ECOKI M PROTEIN
    C: TYPE I RESTRICTION ENZYME ECOKI M PROTEIN
    D: GENE 0.3 PROTEIN
    E: GENE 0.3 PROTEIN

    198 kDa, 5 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    197,6075
    Polyers197,6075
    Non-polymers00
    Water0

    Omokage search
    #1idetical with deposited unit / defined by author&software (PISA) / Symmetry operations: (identity)x1
    Download

    -
    Components

    #1polypeptide(L) / TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN / HSDS TYPE I DNA RESTRICTION SPECIFICITY SUBUNIT, S.ECOKI, TYPE I RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN, S PROTEIN / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P05719, EC: 3.1.21.3
    #2polypeptide(L) / TYPE I RESTRICTION ENZYME ECOKI M PROTEIN / HSDM TYPE I DNA RESTRICTION METHYLTRANSFERASE SUBUNIT, M.ECOKI / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P08957, EC: 3.1.21.3, EC: 2.1.1.72
    #3polypeptide(L) / GENE 0.3 PROTEIN / OCR ANTIRESTRICTION PROTEIN, DNA MIMIC / Source: ENTEROBACTERIA PHAGE T7 (gene. exp.) / References: UniProt: P03775

    +
    Experimental details

    -
    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: NEGATIVE STAIN

    -
    Sample preparation

    Assembly of specimenName: M.ECOKI WITH OCR / Aggregation state: PARTICLE
    Buffer solutionName: 20MM TRIS-CL, 100 MM NACL
    Sample preparationpH: 4.7 / Sample conc.: 0.05 mg/ml
    Specimen supportDetails: CARBON

    -
    Electron microscopy imaging

    MicroscopyMicroscope model: OTHER / Date: Feb 1, 2008
    Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 80 kV / Electron dose: 25 e/A2 / Illumination mode: MEDIUM DOSE
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Calibrated magnification: 39500 X / Nominal defocus max: 870 nm / Nominal defocus min: 275 nm / Cs: 2 mm
    Specimen holderTemperature: 294 K
    CameraType: KODAK SO163 FILM
    Radiation wavelengthRelative weight: 1

    -
    Processing

    Image selectionSoftware name: IMAGIC, EMAN, MRC,UROX,CHIMERA / Number of particles: 17807
    3D reconstructionResolution: 18 A / Nominal pixel size: 3.12 A/pix / Actual pixel size: 3.12 A/pix / Magnification calibration: TMV / CTF correction method: FILTERED AT FIRST ZERO
    Details: HSDM N-TERMINAL DOMAIN RETRACED FROM PDB ENTRY 2AR0. DISORDERED C-TERMINUS OF HSDM MODELLED INTO DENSITY.
    Atomic model buildingMethod: UROX / Ref protocol: RIGID BODY / Ref space: REAL
    Least-squares processHighest resolution: 18 A
    Refine hist #LASTHighest resolution: 18 A
    Number of atoms included #LASTProtein: 13725 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 13725

    +
    About Yorodumi

    -
    News

    -
    Sep 15, 2016. EM Navigator & Yorodumi renewed

    EM Navigator & Yorodumi renewed

    • New versions of EM Navigator and Yorodumi started

    Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

    -
    Aug 31, 2016. New EM Navigator & Yorodumi

    New EM Navigator & Yorodumi

    • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
    • Current version will continue as 'legacy version' for some time.

    Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

    +
    Apr 13, 2016. Omokage search got faster

    Omokage search got faster

    • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
    • Enjoy "shape similarity" of biomolecules, more!

    Related info.: Omokage search

    +
    Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

    Read more

    -
    Yorodumi

    Thousand views of thousand structures

    • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
    • All the functionalities will be ported from the levgacy version.
    • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

    Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

    Read more