5VOI Transcription Dna Rna date May 02, 2017
title X-Ray Crystal Structure Of Bacterial Rna Polymerase And Pyrg Complex
authors K.S.Murakami, Y.Shin, C.L.Turnbough Jr, V.Molodtsov
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
 Organism_scientific: Thermus Thermophilus (Strain Hb27 At 163 Dsm 7039);
Organism_taxid: 262724
Strain: Hb27 Atcc Baa-163 Dsm 7039

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C
Synonym: Rnap Subunit Beta,Rna Polymerase Subunit Beta,Tran Subunit Beta;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D
Synonym: Rnap Subunit Beta',Rna Polymerase Subunit Beta', Transcriptase Subunit Beta';
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Omega
Chain: E
Synonym: Rnap Omega Subunit,Rna Polymerase Omega Subunit, Transcriptase Subunit Omega;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Pyrg Promoter
Chain: G
Engineered: Yes
Synthetic: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423

Molecule: Pyrg Promoter
Chain: H
Engineered: Yes
Synthetic: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
symmetry Space Group: C 1 2 1
R_factor 0.192 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
183.180 103.474 294.444 90.00 99.14 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


F
  • bacterial sigma factor activ...


    • Primary referenceX-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway., Murakami KS, Shin Y, Turnbough CL Jr, Molodtsov V, Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):8211-8216. doi:, 10.1073/pnas.1702741114. Epub 2017 Jun 26. PMID:28652344
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1199 Kb) [Save to disk]
  • Biological Unit Coordinates (5voi.pdb1.gz) 1188 Kb
  • LPC: Ligand-Protein Contacts for 5VOI
  • CSU: Contacts of Structural Units for 5VOI
  • Structure Factors (3505 Kb)
  • Retrieve 5VOI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VOI from S2C, [Save to disk]
  • Re-refined 5voi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5VOI 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 5VOI
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5voi_G] [5voi_C] [5voi_H] [5voi_F] [5voi_B] [5voi_E] [5voi_D] [5voi] [5voi_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5VOI
  • Community annotation for 5VOI at PDBWiki (http://pdbwiki.org)

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