4AYB Transferase date Jun 19, 2012
title Rnap At 3.2ang
authors M.N.Wojtas, M.Mogni, O.Millet, S.D.Bell, N.G.A.Abrescia
compound source
Molecule: Dna-Directed Rna Polymerase
Chain: A
Ec: 2.7.7.6
Other_details: Rpo1n Subunit
 Organism_scientific: Sulfolobus Shibatae
Organism_common: Archaea
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase
Chain: B
Ec: 2.7.7.6
Other_details: Rpo2
Organism_scientific: Sulfolobus Shibatae
Organism_common: Archaea
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase
Chain: C
Ec: 2.7.7.6
Other_details: Rpo1c
Organism_scientific: Sulfolobus Shibatae
Organism_common: Archaea
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase
Chain: D
Ec: 2.7.7.6
Other_details: Rpo3
Organism_scientific: Sulfolobus Shibatae
Organism_common: Archaea
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase
Chain: E
Ec: 2.7.7.6
Other_details: Rpo7
Organism_scientific: Sulfolobus Shibatae
Organism_common: Archaea
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase
Chain: F
Ec: 2.7.7.6
Other_details: Rpof
Organism_scientific: Sulfolobus Shibatae
Organism_common: Archaea
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase
Chain: G
Ec: 2.7.7.6
Other_details: Rpo8
Organism_scientific: Sulfolobus Shibatae
Organism_common: Archaea
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase
Chain: H
Ec: 2.7.7.6
Other_details: Rpo5
Organism_scientific: Sulfolobus Shibatae
Organism_common: Archaea
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase
Chain: K
Ec: 2.7.7.6
Other_details: Rpo6
Organism_scientific: Sulfolobus Shibatae
Organism_common: Archaea
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase
Chain: L
Ec: 2.7.7.6
Other_details: Rpo11
Organism_scientific: Sulfolobus Shibatae
Organism_common: Archaea
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase
Chain: N
Ec: 2.7.7.6
Other_details: Rpo10
Organism_scientific: Sulfolobus Shibatae
Organism_common: Archaea
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase
Chain: P
Ec: 2.7.7.6
Other_details: Rpo12
Organism_scientific: Sulfolobus Shibatae
Organism_common: Archaea
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase
Chain: Q
Ec: 2.7.7.6
Other_details: Rpo13
Organism_scientific: Sulfolobus Shibatae
Organism_common: Archaea
Organism_taxid: 2286
symmetry Space Group: P 21 21 2
R_factor 0.243 R_Free 0.301
crystal
cell
length a length b length c angle alpha angle beta angle gamma
195.725 212.415 128.757 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand MG, SF4, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


H


K


L


N


P


Primary referenceStructural and functional analyses of the interaction of archaeal RNA polymerase with DNA., Wojtas MN, Mogni M, Millet O, Bell SD, Abrescia NG, Nucleic Acids Res. 2012 Jul 30. PMID:22848102
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1627 Kb) [Save to disk]
  • Biological Unit Coordinates (4ayb.pdb1.gz) 1616 Kb
  • LPC: Ligand-Protein Contacts for 4AYB
  • CSU: Contacts of Structural Units for 4AYB
  • Structure Factors (717 Kb)
  • Retrieve 4AYB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4AYB from S2C, [Save to disk]
  • Re-refined 4ayb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4AYB 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 4AYB
  • 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 4AYB, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ayb_N] [4ayb_G] [4ayb_A] [4ayb_E] [4ayb_P] [4ayb_B] [4ayb_F] [4ayb_L] [4ayb_H] [4ayb_Q] [4ayb_D] [4ayb] [4ayb_K] [4ayb_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4AYB: [RNA_pol_Rpb6] [RPOLA_N] [RPOLCX] [RPOLD] [S1 ] by SMART
    • Other resources with information on 4AYB
  • Community annotation for 4AYB at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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