5VI8 Transcription date Apr 14, 2017
title Structure Of A Mycobacterium Smegmatis Transcription Initiat Complex With An Upstream-Fork Promoter Fragment
authors E.A.Hubin, E.A.Campbell, S.A.Darst
compound source
Molecule: Rna Polymerase-Binding Protein Rbpa
Chain: J
Engineered: Yes
 Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
Gene: Rbpa, Msmeg_3858, Msmei_3768
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

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: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

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: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

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: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

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: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F
Engineered: Yes
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
Gene: Rpod, Siga, Msmeg_2758, Msmei_2690
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693

Molecule: Dna (31-Mer)
Chain: O
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (26-Mer)
Chain: P
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: T
Fragment: C-Terminal Residues 251-350
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
symmetry Space Group: P 1 21 1
R_factor 0.240 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
133.012 161.633 139.211 90.00 107.72 90.00
method X-Ray Diffractionresolution 2.76 Å
ligand EDO, MG, SO4, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene MSMEG ; MSMEG ; MSMEI ; MSMEI
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


F
  • bacterial sigma factor activ...


    • J


    T


    Primary referenceStructural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures., Hubin EA, Lilic M, Darst SA, Campbell EA, Nat Commun. 2017 Jul 13;8:16072. doi: 10.1038/ncomms16072. PMID:28703128
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (545 Kb) [Save to disk]
  • Biological Unit Coordinates (5vi8.pdb1.gz) 533 Kb
  • LPC: Ligand-Protein Contacts for 5VI8
  • CSU: Contacts of Structural Units for 5VI8
  • Structure Factors (3042 Kb)
  • Retrieve 5VI8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VI8 from S2C, [Save to disk]
  • Re-refined 5vi8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5VI8 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 5VI8
  • 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: [5vi8_D] [5vi8_C] [5vi8_P] [5vi8_J] [5vi8_T] [5vi8_O] [5vi8_E] [5vi8_A] [5vi8_B] [5vi8_F] [5vi8]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5VI8
  • Community annotation for 5VI8 at PDBWiki (http://pdbwiki.org)

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