6VVT Transcription,Transferase Dna Antibiotic date Feb 18, 2020
title Crystal Structure Of A Mycobacterium Smegmatis Transcription Initiation Complex With Rifampicin-Resistant Rna Polymerase Antibiotic Sorangicin
authors M.Lilic, S.A.Darst, E.A.Campbell
compound source
Molecule: Rna Polymerase-Binding Protein Rbpa
Chain: J
Organism_scientific: Mycolicibacterium Smegmatis (Strain At Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

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: Mycolicibacterium Smegmatis (Strain At 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: Mycolicibacterium Smegmatis (Strain At 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: Mycolicibacterium Smegmatis (Strain At 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: Mycolicibacterium Smegmatis (Strain At Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F
Engineered: Yes

Organism_scientific: Mycolicibacterium Smegmatis (Strain At Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
Gene: Siga, Msmeg_2758
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768

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 0.240 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
129.217 162.212 136.295 90.00 111.36 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand EDO, SO4, 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] (499 Kb) [Save to disk]
  • Biological Unit Coordinates (6vvt.pdb1.gz) 477 Kb
  • LPC: Ligand-Protein Contacts for 6VVT
  • CSU: Contacts of Structural Units for 6VVT
  • Structure Factors (2236 Kb)
  • Retrieve 6VVT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6VVT from S2C, [Save to disk]
  • View 6VVT 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 6VVT
  • 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
  • Fold representative 6vvt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6vvt_C] [6vvt_O] [6vvt_D] [6vvt_B] [6vvt_A] [6vvt_J] [6vvt_F] [6vvt_P] [6vvt_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6VVT
  • Community annotation for 6VVT at PDBWiki (http://pdbwiki.org)

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