Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - PDB-2b6o: electron crystallographic structure of lens Aquaporin-0 (AQP0) (l... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: PDB / ID: 2b6o
    Titleelectron crystallographic structure of lens Aquaporin-0 (AQP0) (lens MIP) at 1.9A resolution, in a closed pore state
    DescriptorLens fiber major intrinsic protein
    Keywordsmembrane protein / aquaporin-0 junctions / AQP0 / lens MIP / lipid-protein interactions / membrane / lipid bilayer / closed water pore / electron crystallography
    Specimen sourceOvis aries / mammal / sheep /
    MethodElectron crystallography (1.9 A resolution / Molecular replacement)
    AuthorsGonen, T. / Cheng, Y. / Sliz, P. / Hiroaki, Y. / Fujiyoshi, Y. / Harrison, S.C. / Walz, T.
    CitationNature, 2005, 438, 633-638

    Nature, 2005, 438, 633-638 StrPapers
    Lipid-protein interactions in double-layered two-dimensional AQP0 crystals.
    Tamir Gonen / Yifan Cheng / Piotr Sliz / Yoko Hiroaki / Yoshinori Fujiyoshi / Stephen C Harrison / Thomas Walz

    DateDeposition: Oct 3, 2005 / Release: Dec 6, 2005 / Last modification: Jul 13, 2011

    -
    Structure visualization

    Movie
    • Biological unit as octameric
    • Imaged by Jmol
    • Download
    • Biological unit as octameric
    • Imaged by Jmol
    • Download
    • 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: Lens fiber major intrinsic protein
    hetero molecules

    34.4 kDa, 10 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    34,38710
    Polyers28,2851
    Non-polymers6,1019
    Water1,42379

    Omokage search
    #1
    A: Lens fiber major intrinsic protein
    hetero molecules
    x 8
    defined by author / 275 kDa, 80 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    275,09380
    Polyers226,2818
    Non-polymers48,81272
    Water1448
    / Symmetry operations: (identity)x1 + (crystal symmetry)x7
    Download / Omokage search
    #2
    A: Lens fiber major intrinsic protein
    hetero molecules
    x 8
    defined by software (PQS)
    Buried area (A2)82930
    Surface area (A2)72410
    ΔGint (kcal/M)-755
    / 275 kDa, 80 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    275,09380
    Polyers226,2818
    Non-polymers48,81272
    Water1448
    / Symmetry operations: (identity)x1 + (crystal symmetry)x7
    Download / Omokage search

    -
    Components

    #1polypeptide(L) / Lens fiber major intrinsic protein / Aquaporin-0 / Source: Ovis aries (gene. exp.) / References: UniProt: Q6J8I9
    #2ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
    #3ChemComp-HOH / water

    +
    Experimental details

    -
    Experiment

    ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 286

    -
    Sample preparation

    CrystalDensity Matthews: 3.03 A3/Da / Density percent sol: 59.44 %
    Crystal growTemp: 300 K / Method: MICRODIALYSIS / pH: 6
    Details: 20mM MES pH 6.0, 50mM MgCl2, 5mM DTT, MICRODIALYSIS, temperature 300K

    -
    Data collection

    DiffractionMean temperature: 281 K
    SourceSource: ELECTRON MICROSCOPE / Type: JEM3000SFF
    DetectorType: GATAN / Details: 4k X 4k / Detector: CCD / Collection date: Dec 1, 2003
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1
    ReflectionB iso Wilson estimate: 18.1 A^2 / D resolution high: 1.9 A / D resolution low: 20 A / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.166 / Redundancy: 5.7 / Percent possible obs: 80
    Reflection shellHighest resolution: 1.9 A / Lowest resolution: 2 A / Redundancy: 2.5 / Percent possible all: 70.5

    -
    Processing

    Software
    NameVersionClassification
    GATANdata collection
    GATANdata reduction
    CNSmodel building
    CNS1.1refinement
    ComputingData reduction ds: GATAN / Data reduction ii: GATAN / Structure refinement: CNS 1.1 / Structure solution: CNS
    Image selectionSoftware name: CNS 1.1
    RefineMethod to determine structure: MOLECULAR REPLACEMENT
    Starting model: 1SOR - aquaporin-0 (MIP) strructure determined by electron crystallography
    R Free selection details: RANDOM / Data cutoff high absF: 2606056.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
    Displacement parametersB iso mean: 58.4 A2 / Aniso B11: -7.32 A2 / Aniso B12: 0 A2 / Aniso B13: 0 A2 / Aniso B22: -7.32 A2 / Aniso B23: 0 A2 / Aniso B33: 14.64 A2
    Least-squares processR factor R free: 0.299 / R factor R free error: 0.008 / R factor R work: 0.258 / Highest resolution: 1.9 A / Lowest resolution: 5 A / Number reflection R free: 1580 / Number reflection all: 16180 / Number reflection obs: 14600 / Percent reflection R free: 9.8
    Refine analyzeLuzzati coordinate error free: 0.42 A / Luzzati coordinate error obs: 0.37 A / Luzzati d res low obs: 5 A / Luzzati sigma a free: 0.65 A / Luzzati sigma a obs: 0.63 A
    Refine hist #LASTHighest resolution: 1.9 A / Lowest resolution: 5 A
    Number of atoms included #LASTProtein: 1783 / Nucleic acid: 0 / Ligand: 349 / Solvent: 79 / Total: 2211
    Refine LS restraints
    Refine idTypeDev idealDev ideal target
    ELECTRON CRYSTALLOGRAPHYo_bond_d0.016
    ELECTRON CRYSTALLOGRAPHYo_angle_deg1.9
    ELECTRON CRYSTALLOGRAPHYo_dihedral_angle_d19.8
    ELECTRON CRYSTALLOGRAPHYo_improper_angle_d1.25
    ELECTRON CRYSTALLOGRAPHYo_mcbond_it1.531.5
    ELECTRON CRYSTALLOGRAPHYo_mcangle_it2.612
    ELECTRON CRYSTALLOGRAPHYo_scbond_it1.632
    ELECTRON CRYSTALLOGRAPHYo_scangle_it2.442.5
    Xplor file
    Refine idSerial noParam fileTopol file
    ELECTRON CRYSTALLOGRAPHY1protein_rep.paramprotein.top
    ELECTRON CRYSTALLOGRAPHY2water_rep.paramwater.top
    ELECTRON CRYSTALLOGRAPHY3dmpc.paramdmpc_all_final.top

    +
    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