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    - PDB-487d: SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MA... -

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    Basic information

    Entry
    Database: PDB / ID: 487d
    TitleSEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION
    DescriptorSEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION
    KeywordsRIBOSOME / LARGE RIBOSOMAL SUBUNIT / RIBOSOMAL PROTEIN / PROTEIN BIOSYNTHESIS / EM-RECONSTRUCTION / ATOMIC STRUCTURE / 3D ARRANGEMENT / FITTING
    Specimen sourceThermus thermophilus / bacteria / thermophilic
    Geobacillus stearothermophilus / bacteria / thermophilic
    Thermotoga maritima / bacteria / thermophilic
    Escherichia coli / bacteria /
    MethodElectron microscopy (7.5 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsBrimacombe, R. / Mueller, F.
    CitationJ. Mol. Biol., 2000, 298, 35-59

    primary. J. Mol. Biol., 2000, 298, 35-59 StrPapers
    The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution.
    F Mueller / I Sommer / P Baranov / R Matadeen / M Stoldt / J Wöhnert / M Görlach / M van Heel / R Brimacombe

    #1. Cell(Cambridge,Mass.), 1999, 97, 491-
    A Detailed View of a Ribosomal Active Site: The Structure of the Gtpase Center at 2.6 Angstroms Resolution.
    Wimberly, B.T. / Guymon, R. / Mc Cutcheon, J.P. / White, S. / Ramakrishnan, V.

    #2. Embo J., 1999, 18, 6508-
    The NMR Structure of the 5S Rrna E-Domain-Protein C25 Complex Shows Pre-Formed and Induced Recognition.
    Stoldt, M. / Woehnert, J. / Ohlenschlaeger, O. / Goerlach, M. / Brown, L.R.

    #3. Embo J., 1999, 18, 1459-
    The Three-Dimensional Structure of the RNA-Binding Domain of Ribosomal Protein L2; a Protein at the Peptidyl Transferase Center of the Ribosome.
    Nakagawa, A. / Nakashima, T. / Taniguchi, M. / Hosaka, H. / Kimura, M. / Tanaka, I.

    #4. J.Mol.Biol., 1996, 264, 1058-
    Ribosomal Protein L9: A Structure Determination by the Combined Use of X-Ray Crystallography and NMR Spectroscopy.
    Hoffman, D.W. / Cameron, C.S. / Davies, C. / White, S.W. / Ramakrishnan, V.

    #5. Embo J., 1996, 15, 1350-
    Crystal Structure of the RNA Binding Ribosomal Protein L1 from Thermus Thermophilus.
    Nikonov, S. / Nevskaya, N. / Eliseikina, I. / Fomenkova, N. / Nikulin, A. / Ossina, N. / Garber, M. / Jonsson, B.H. / Briand, C. / Al-Karadaghi, S. / Svensson, A. / Aevarsson, A. / Liljas, A.

    #6. Structure, 1996, 4, 55-
    The Crystal Structure of Ribosomal Protein L14 Reveals an Important Organizational Component of the Translational Apparatus.
    Davies, C. / White, S.W. / Ramakrishnan, V.

    #7. Embo J., 1993, 12, 4901-
    Ribosomal Protein L6: Structural Evidence of Gene Duplication from a Primitive RNA Binding Proetin.
    Golden, B.L. / Ramakrishnan, V. / White, S.W.

    DateDeposition: Feb 23, 2000 / Release: Apr 10, 2000 / Last modification: Feb 24, 2009

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    Assembly

    Deposited unit
    H: PROTEIN (50S L1 RIBOSOMAL PROTEIN)
    I: PROTEIN (50S L2 RIBOSOMAL PROTEIN)
    J: PROTEIN (50S L6 RIBOSOMAL PROTEIN)
    K: PROTEIN (50S L9 RIBOSOMAL PROTEIN)
    L: PROTEIN (50S L11 RIBOSOMAL PROTEIN)
    M: PROTEIN (50S L14 RIBOSOMAL PROTEIN)
    N: PROTEIN (50S L25 RIBOSOMAL PROTEIN)
    hetero molecules

    112 kDa, 9 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    111,6849
    Polyers111,6227
    Non-polymers622
    Water0

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

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    Polypeptide(L) , 7 types, 7 molecules HIJKLMN

    #1polypeptide(L) / PROTEIN (50S L1 RIBOSOMAL PROTEIN) / Source: Thermus thermophilus (gene. exp.) / References: UniProt: P27150
    #2polypeptide(L) / PROTEIN (50S L2 RIBOSOMAL PROTEIN) / Source: Geobacillus stearothermophilus (gene. exp.) / References: UniProt: P04257
    #3polypeptide(L) / PROTEIN (50S L6 RIBOSOMAL PROTEIN) / Source: Geobacillus stearothermophilus (gene. exp.) / References: UniProt: P02391
    #4polypeptide(L) / PROTEIN (50S L9 RIBOSOMAL PROTEIN) / Source: Geobacillus stearothermophilus (gene. exp.) / References: UniProt: P02417
    #5polypeptide(L) / PROTEIN (50S L11 RIBOSOMAL PROTEIN) / Source: Thermotoga maritima (gene. exp.) / References: UniProt: P29395
    #6polypeptide(L) / PROTEIN (50S L14 RIBOSOMAL PROTEIN) / Source: Geobacillus stearothermophilus (gene. exp.) / References: UniProt: P04450
    #7polypeptide(L) / PROTEIN (50S L25 RIBOSOMAL PROTEIN) / Source: Escherichia coli (gene. exp.) / References: UniProt: P02426

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    Non-polymers , 2 types, 2 molecules

    #8ChemComp-NH2 / AMINO GROUP
    #9ChemComp-FMT / FORMIC ACID

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    Experimental details

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    Experiment

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

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    Sample preparation

    Assembly of specimenAggregation state: PARTICLE
    CrystalDescription: THE CRYST1 AND SCALE RECORDS ARE MEANINGLESS.

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    Processing

    EM single particle entitySymmetry type: ASYMMETRIC
    Atomic model buildingDetails: OTHER REFINEMENT REMARKS: CRYO-EM RECONSTRUCTION THIS FILE HAS BEEN GENERATED BY THE USE OF ALL RELEVANT BIOCHEMICAL CONSTRAINTS AND THE CONSTRAINTS GIVEN BY THE ELECTRON DENSITY CONTOUR OF THE RIBOSOME, WHICH WAS DERIVED FROM THE CRYO-ELECTRON MICROSCOPIC RECONSTRUCTION.
    Ref space: REAL
    Atomic model building
    PDB-ID 3D fitting idID
    487D
    11
    487D
    12
    487D
    13
    Least-squares processHighest resolution: 7.5 A
    Refine hist #LASTHighest resolution: 7.5 A
    Number of atoms included #LASTProtein: 7821 / Nucleic acid: 0 / Ligand: 4 / Solvent: 0 / Total: 7825

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