2WAQ Transcription date Feb 11, 2009
title The Complete Structure Of The Archaeal 13-Subunit Dna-Direct Polymerase
authors Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P. S.D.Bell, N.G.A.Abrescia
compound source
Molecule: Dna-Directed Rna Polymerase Rpo1n Subunit
Chain: A
 Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo2 Subunit
Chain: B
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo1c Subunit
Chain: C
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo3 Subunit
Chain: D
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo7 Subunit
Chain: E
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo4 Subunit
Chain: F
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo8 Subunit
Chain: G
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo5 Subunit
Chain: H
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo6 Subunit
Chain: K
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo11 Subunit
Chain: L
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo10 Subunit
Chain: N
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo12 Subunit
Chain: P
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo13 Subunit
Chain: Q
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286
symmetry Space Group: P 21 21 2
R_factor 0.271 R_Free 0.341
crystal
cell
length a length b length c angle alpha angle beta angle gamma
193.501 212.620 128.998 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.35 Å
ligand F3S, MG, ZN enzyme
note 2WAQ is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


H


K


L


N


P


Primary referenceEvolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure., Korkhin Y, Unligil UM, Littlefield O, Nelson PJ, Stuart DI, Sigler PB, Bell SD, Abrescia NG, PLoS Biol. 2009 May 5;7(5):e102. PMID:19419240
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1097 Kb) [Save to disk]
  • Biological Unit Coordinates (2waq.pdb1.gz) 1090 Kb
  • LPC: Ligand-Protein Contacts for 2WAQ
  • CSU: Contacts of Structural Units for 2WAQ
  • Likely Quarternary Molecular Structure file(s) for 2WAQ
  • Structure Factors (449 Kb)
  • Retrieve 2WAQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2WAQ from S2C, [Save to disk]
  • Re-refined 2waq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2WAQ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 2WAQ
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2WAQ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2waq_A] [2waq_C] [2waq_F] [2waq] [2waq_B] [2waq_Q] [2waq_E] [2waq_D] [2waq_G] [2waq_P] [2waq_H] [2waq_K] [2waq_L] [2waq_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2WAQ: [RNA_pol_Rpb6] [RPOLA_N] [RPOLCX] [RPOLD] [S1 ] by SMART
    • Other resources with information on 2WAQ
  • Community annotation for 2WAQ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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