4PII

Crystal structure of hypothetical protein PF0907 from pyrococcus furiosus solved by sulfur SAD using Swiss light source data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 co ...

    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.,National Centre for Biological Sciences, Bangalore, India.,Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.,Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland.,Swiss Light Source at Paul Scherrer Institut, Villigen, Switzerland.,Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach an der Riss, Germany.,Department of Experimental Oncology, European Institute of Oncology, Milan, Italy.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.,Laboratory of Biological Chemistry, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-glycosylase/DNA lyase
A
250Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Find proteins for Q8U2D5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U2D5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.173 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 98.430α = 90.00
b = 98.430β = 90.00
c = 65.230γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
Cootmodel building
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Derived calculations, Refinement description