4OIN Transcription, Transferase Antibiotic date Jan 20, 2014
title Crystal Structure Of Thermus Thermophilus Transcription Init Complex Soaked With Ge23077
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 G)-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 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
183.770 103.200 294.770 90.00 99.18 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 0QZ, 2RA, 2TL, DSN, DVA, FGL, MB8, MG, R2T, 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] (603 Kb) [Save to disk]
  • Biological Unit Coordinates (4oin.pdb1.gz) 593 Kb
  • LPC: Ligand-Protein Contacts for 4OIN
  • CSU: Contacts of Structural Units for 4OIN
  • Structure Factors (2156 Kb)
  • Retrieve 4OIN in mmCIF format [Save to disk]
  • Re-refined 4oin structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4OIN 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 4OIN
  • 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 4OIN, from MSDmotif at EBI
  • Fold representative 4oin from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4oin_G] [4oin_E] [4oin_C] [4oin_D] [4oin_H] [4oin_A] [4oin_F] [4oin] [4oin_B] [4oin_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4OIN: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4OIN
  • Community annotation for 4OIN at PDBWiki (http://pdbwiki.org)

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