4R8U

S-SAD structure of DINB-DNA Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Fast native-SAD phasing for routine macromolecular structure determination

Weinert, T.Olieric, V.Waltersperger, S.Panepucci, E.Chen, L.Zhang, H.Zhou, D.Rose, J.Ebihara, A.Kuramitsu, S.Li, D.Howe, N.Schnapp, G.Pautsch, A.Bargsten, K.Prota, A.E.Surana, P.Kottur, J.Nair, D.T.Basilico, F.Cecatiello, V.Pasqualato, S.Boland, A.Weichenrieder, O.Wang, B.C.Steinmetz, M.O.Caffrey, M.Wang, M.

(2015) Nat Methods 12: 131-133

  • DOI: 10.1038/nmeth.3211
  • Primary Citation of Related Structures:  
    4TN8, 4TNO, 4PGO, 4PII, 4WAU, 4WAB, 4WBX, 4WBQ, 4R8T, 4R8U

  • PubMed Abstract: 
  • We describe a data collection method that uses a single crystal to solve X-ray structures by native SAD (single-wavelength anomalous diffraction). We solved the structures of 11 real-life examples, including a human membrane protein, a protein-DNA complex and a 266-kDa multiprotein-ligand complex, using this method ...

    We describe a data collection method that uses a single crystal to solve X-ray structures by native SAD (single-wavelength anomalous diffraction). We solved the structures of 11 real-life examples, including a human membrane protein, a protein-DNA complex and a 266-kDa multiprotein-ligand complex, using this method. The data collection strategy is suitable for routine structure determination and can be implemented at most macromolecular crystallography synchrotron beamlines.


    Organizational Affiliation

    Swiss Light Source at Paul Scherrer Institut, Villigen, Switzerland.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVA340Escherichia coli K-12Mutation(s): 0 
Gene Names: b0231dinBdinPJW0221
EC: 2.7.7.7
Find proteins for Q47155 (Escherichia coli (strain K12))
Explore Q47155 
Go to UniProtKB:  Q47155
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVB338Escherichia coli K-12Mutation(s): 0 
Gene Names: b0231dinBdinPJW0221
EC: 2.7.7.7
Find proteins for Q47155 (Escherichia coli (strain K12))
Explore Q47155 
Go to UniProtKB:  Q47155
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNAC [auth V], E [auth C]17synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      DNAD [auth W]18synthetic construct
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 5
        MoleculeChainsLengthOrganismImage
        DNAF [auth D]16synthetic construct
        Small Molecules
        Ligands 2 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        1FZ
        Query on 1FZ

        Download Ideal Coordinates CCD File 
        H [auth A], I [auth B]5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine
        C10 H18 N3 O13 P3
        YRKUYVYMPXAOAT-XLPZGREQSA-N
         Ligand Interaction
        MG
        Query on MG

        Download Ideal Coordinates CCD File 
        G [auth A], J [auth B]MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.30 Å
        • R-Value Free: 0.220 
        • R-Value Work: 0.181 
        • R-Value Observed: 0.183 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 86.95α = 90
        b = 57.21β = 94.69
        c = 110.6γ = 90
        Software Package:
        Software NamePurpose
        PHASERphasing
        PHENIXrefinement
        d*TREKdata reduction
        d*TREKdata scaling

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2015-01-14
          Type: Initial release
        • Version 1.1: 2015-08-12
          Changes: Database references
        • Version 1.2: 2015-09-02
          Changes: Source and taxonomy
        • Version 1.3: 2017-11-22
          Changes: Refinement description