1RYQ

Putative DNA-directed RNA polymerase, subunit e'' from Pyrococcus Furiosus Pfu-263306-001


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Parameter-space screening: a powerful tool for high-throughput crystal structure determination.

Liu, Z.J.Lin, D.Tempel, W.Praissman, J.L.Rose, J.P.Wang, B.C.

(2005) Acta Crystallogr.,Sect.D 61: 520-527

  • DOI: 10.1107/S0907444905003239

  • PubMed Abstract: 
  • The determination of protein structures on a genomic scale requires both computing capacity and efficiency increases at many stages along the complex process. By combining bioinformatics workflow-management techniques, cluster-based computing and pop ...

    The determination of protein structures on a genomic scale requires both computing capacity and efficiency increases at many stages along the complex process. By combining bioinformatics workflow-management techniques, cluster-based computing and popular crystallographic structure-determination software packages, an efficient and powerful new tool for structural biology/genomics has been developed. Using the workflow manager and a simple web interface, the researcher can, in a few easy steps, set up hundreds of structure-determination jobs, each using a slightly different set of program input parameters, thus efficiently screening parameter space for the optimal input-parameter combination, i.e. a set of parameters that leads to a successful structure determination. Upon completion, results from the programs are harvested, analyzed, sorted based on success and presented to the user via the web interface. This approach has been applied with success in more than 30 cases. Examples of successful structure determinations based on single-wavelength scattering (SAS) are described and include cases where the 'rational' crystallographer-based selection of input parameters values had failed.


    Related Citations: 
    • The high-throughput protein-to-structure pipeline at SECSG
      Liu, Z.-J.,Tempel, W.,Ng, J.D.,Lin, D.,Shah, A.K.,Chen, L.,Horanyi, P.S.,Habel, J.E.,Kataeva, I.A.,Xu, H.,Yang, H.,Chang, J.C.,Huang, L.,Chang, S.H.,Zhou, W.,Lee, D.,Praissman, J.L.,Zhang, H.,Newton, M.G.,Rose, J.P.,Richardson, J.S.,Richardson, D.C.,Wang, B.C.
      (2005) Acta Crystallogr.,Sect.D 61: 679


    Organizational Affiliation

    Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia, USA. liu@secsg.uga.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase, subunit e''
A
69Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: spt4
Find proteins for Q8U440 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U440
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.193 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 45.534α = 90.00
b = 45.534β = 90.00
c = 50.760γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description