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    - PDB-4a8c: Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in comp... -

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    Basic information

    Entry
    Database: PDB / ID: 4a8c
    TitleSymmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with a binding peptide
    DescriptorPERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ (E.C.3.4.21.107)
    KeywordsHYDROLASE / CHAPERONE
    Specimen sourceEscherichia coli / bacteria /
    MethodElectron microscopy (7.5 A resolution / Single particle / Vitreous ice)
    AuthorsMalet, H. / Canellas, F. / Sawa, J. / Yan, J. / Thalassinos, K. / Ehrmann, M. / Clausen, T. / Saibil, H.R.
    CitationNat. Struct. Mol. Biol., 2012, 19, 152-157

    Nat. Struct. Mol. Biol., 2012, 19, 152-157 StrPapers
    Newly folded substrates inside the molecular cage of the HtrA chaperone DegQ.
    Hélène Malet / Flavia Canellas / Justyna Sawa / Jun Yan / Konstantinos Thalassinos / Michael Ehrmann / Tim Clausen / Helen R Saibil

    DateDeposition: Nov 20, 2011 / Release: Jan 11, 2012 / Last modification: Feb 15, 2012

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    Assembly

    Deposited unit
    A: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
    B: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
    C: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
    D: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
    E: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
    F: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
    G: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
    H: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
    I: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
    J: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
    K: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
    L: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ

    547 kDa, 12 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    546,51812
    Polyers546,51812
    Non-polymers00
    Water0

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    #1idetical with deposited unit / defined by author / Symmetry operations: (identity)x1
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    Components

    #1polypeptide(L) / PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ / PROTEASE DO, DEGQ / Mutation: YES / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P39099, EC: 3.4.21.107

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE

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    Sample preparation

    Assembly of specimenName: ESCHERICHIA COLI DEGQ 12- MER IN COMPLEX WITH A BINDING PEPTIDE
    Aggregation state: PARTICLE
    Buffer solutionName: 20 MM HEPES/NAOH, 150 MM NACL
    Sample preparationpH: 7.5 / Sample conc.: 0.2 mg/ml
    Specimen supportDetails: CARBON
    VitrificationDetails: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- MANUAL PLUNGER, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING,

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI TECNAI F20 / Details: LOW DOSE MODE
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
    Specimen holderTemperature: 91 K / Tilt angle max: 0 deg. / Tilt angle min: -0.1 deg.
    CameraType: KODAK SO163 FILM
    EM image scansNumber digital images: 110
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: IMAGIC-5, SPIDER / Number of particles: 29432
    EM single particle entitySymmetry type: MIXED SYMMETRY
    3D reconstructionMethod: COMMON LINE, PROJECTION MATCHING / Resolution: 7.5 A / Nominal pixel size: 1.4 A/pix / Actual pixel size: 1.4 A/pix / CTF correction method: PHASE FLIPPING, FULL CTF CORRECTION
    Details: DEGQ 12-MER WERE OBTAINED IN PRESENCE OF A PEPTIDE. THE PEPTIDE SEQUENCE IS SPMFKGVLDMMYGGMRGYQV THE NUMBER OF PEPTIDES BOUND TO DEGQ 12-MER IS UNKNOWN. THE PEPTIDES ARE NOT MODELLED DUE TO THE RESOLUTION OF THE MAP. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1983. (DEPOSITION ID: 10374).
    Atomic model buildingMethod: RIGID BODY AND FLEXIBLE FITTING / Ref protocol: X-RAY / Ref space: REAL / Target criteria: CROSS-CORRELATION, ENERGY
    Least-squares processHighest resolution: 7.5 A
    Refine hist #LASTHighest resolution: 7.5 A
    Number of atoms included #LASTProtein: 4740 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 4740

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