6VVZ Transcription,Transferase Dna Antibiotic date Feb 18, 2020
title Mycobacterium Tuberculosis Rnap S456l Mutant Transcription I Intermediate Structure With Sorangicin
authors M.Lilic, H.Boyaci, J.Chen, S.A.Darst, E.A.Campbell
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
Engineered: Yes
 Organism_scientific: Mycobacterium Tuberculosis
Organism_taxid: 1773
Gene: Rpoa
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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 Tuberculosis
Organism_taxid: 1773
Gene: Rpob, Samea2682864_01701
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
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis
Organism_taxid: 1773
Gene: Rpoc
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis
Organism_taxid: 1773
Gene: Rpoz, Ers007672_03979, Ers007703_04032, Ers007720_047 Ers027652_00548, Ers027654_02543, Ers027656_03959, Ers12436
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F
Synonym: Sigma-A
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis
Organism_taxid: 1773
Gene: Siga, Mysa, Rpod, Rpov
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna Polymerase-Binding Protein Rbpa
Chain: J
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis
Organism_taxid: 1773
Gene: Rbpa
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna Polymerase-Binding Transcription Factor Card
Chain: M
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis
Organism_taxid: 1773
Gene: Card
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (62-Mer)
Chain: P
Organism_scientific: Mycobacterium Tuberculosis
Organism_taxid: 1773

Molecule: Dna (65-Mer)
Chain: O
Organism_scientific: Mycobacterium Tuberculosis
Organism_taxid: 1773
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.72 Å
ligand MG, SRN, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Primary referenceThe antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase., Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Muller R, Mooney R, Landick R, Darst SA, Campbell EA, Proc Natl Acad Sci U S A. 2020 Nov 16. pii: 2013706117. doi:, 10.1073/pnas.2013706117. PMID:33199626
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (541 Kb) [Save to disk]
  • Biological Unit Coordinates (6vvz.pdb1.gz) 532 Kb
  • LPC: Ligand-Protein Contacts for 6VVZ
  • CSU: Contacts of Structural Units for 6VVZ
  • Retrieve 6VVZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6VVZ from S2C, [Save to disk]
    • View 6VVZ 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 6VVZ
  • 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: [6vvz_P] [6vvz_C] [6vvz_M] [6vvz_F] [6vvz_D] [6vvz_A] [6vvz_O] [6vvz_B] [6vvz_E] [6vvz_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6VVZ
  • Community annotation for 6VVZ at PDBWiki (http://pdbwiki.org)

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