6DCF Transcription Dna Antibiotic date May 06, 2018
title Crystal Structure Of A Mycobacterium Smegmatis Transcription Initiation Complex With Rifampicin-Resistant Rna Polymerase To Kanglemycin A
authors M.Lilic, S.A.Darst, E.A.Campbell
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
Engineered: Yes
Mutation: Yes
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
Gene: Rpob, Msmeg_1367, Msmei_1328
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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: Siga, Msmeg_2758
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

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
symmetry Space Group: P 1 21 1
R_factor 0.252 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
129.250 160.909 136.864 90.00 110.75 90.00
method X-Ray Diffractionresolution 3.45 Å
ligand EDO, GLU, KNG, MG, SO4, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


F
  • bacterial sigma factor activ...


    • J


    Primary referenceRifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism., Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I, Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T, Saito K, Braffman N, Fay A, Glickman MS, Darst SA, Campbell EA, Brady SF, Nat Commun. 2018 Oct 8;9(1):4147. doi: 10.1038/s41467-018-06587-2. PMID:30297823
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (481 Kb) [Save to disk]
  • Biological Unit Coordinates (6dcf.pdb1.gz) 468 Kb
  • LPC: Ligand-Protein Contacts for 6DCF
  • CSU: Contacts of Structural Units for 6DCF
  • Structure Factors (1614 Kb)
  • Retrieve 6DCF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6DCF from S2C, [Save to disk]
    • View 6DCF 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 6DCF
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6dcf_C] [6dcf_B] [6dcf_A] [6dcf_P] [6dcf_E] [6dcf_O] [6dcf_D] [6dcf_J] [6dcf_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6DCF
  • Community annotation for 6DCF at PDBWiki (http://pdbwiki.org)

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