4OIR Transcription, Transferase Antibiotic date Jan 20, 2014
title Crystal Structure Of Thermus Thermophilus Rna Polymerase Tra Initiation Complex Soaked With Ge23077 And Rifamycin Sv
authors Y.Zhang, R.H.Ebright, E.Arnold
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
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C
Synonym: Rnap Subunit Beta, Rna Polymerase Subunit Beta, Transcriptase Subunit Beta;
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus
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
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
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna Directed Rna Polymerase Sigma Factor A
Chain: F
Synonym: Rna Polymerase Sigma Factor
Engineered: Yes

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579
Gene: Rpod, Ttha0532
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: 5'-D(Cpcptgpcpaptpcpcpgptpgpapgptp Gpgpg)-3';
Chain: G
Engineered: Yes
Other_details: Promoter Dna Template Strand

Synthetic: Yes

Molecule: 5'-D(Tpaptpapaptpgpgpgpapgpcptpgpt Gpgpaptpgpcpapgpg)-3';
Chain: H
Engineered: Yes
Other_details: Promoter Dna Nontemplate Strand

Synthetic: Yes

Molecule: Ge23077
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Actinomadura Sp.
Organism_taxid: 1989
symmetry Space Group: C 1 2 1
R_factor 0.206 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
183.700 105.010 295.360 90.00 98.79 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand 0QZ, 2RA, 2TL, DSN, DVA, FGL, MB8, MG, R2T, RFV, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


F
  • bacterial sigma factor activ...


  • Primary referenceGE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides., Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH, Elife. 2014 Jan 1;3:e02450. doi: 10.7554/eLife.02450. PMID:24755292
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (595 Kb) [Save to disk]
  • Biological Unit Coordinates (4oir.pdb1.gz) 586 Kb
  • LPC: Ligand-Protein Contacts for 4OIR
  • CSU: Contacts of Structural Units for 4OIR
  • Structure Factors (1423 Kb)
  • Retrieve 4OIR in mmCIF format [Save to disk]
  • Re-refined 4oir structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4OIR 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 4OIR
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4OIR, from MSDmotif at EBI
  • Fold representative 4oir from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4oir_G] [4oir_H] [4oir_C] [4oir_E] [4oir_A] [4oir_I] [4oir_D] [4oir] [4oir_F] [4oir_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4OIR: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4OIR
  • Community annotation for 4OIR at PDBWiki (http://pdbwiki.org)

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