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


Ligand Structure Quality Assessment 


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

  • 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. The data collection strategy is suitable for routine structure determination and can be implemented at most macromolecular crystallography synchrotron beamlines.


  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase IV340Escherichia coli K-12Mutation(s): 0 
Gene Names: b0231dinBdinPJW0221
EC: 2.7.7.7
UniProt
Find proteins for Q47155 (Escherichia coli (strain K12))
Explore Q47155 
Go to UniProtKB:  Q47155
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47155
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase IV338Escherichia coli K-12Mutation(s): 0 
Gene Names: b0231dinBdinPJW0221
EC: 2.7.7.7
UniProt
Find proteins for Q47155 (Escherichia coli (strain K12))
Explore Q47155 
Go to UniProtKB:  Q47155
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47155
Sequence Annotations
Expand
  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNAC [auth V],
E [auth C]
17synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNAD [auth W]18synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
DNAF [auth D]16synthetic construct
Sequence Annotations
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  • Reference Sequence
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

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Ligand Structure Quality Assessment 


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