6JCY Transcription date Jan 30, 2019
title Mycobacterium Tuberculosis Rna Polymerase Transcription Init Open Complex With A Chimeric Ecf Sigma Factor Sighe
authors L.Li, Y.Zhang
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 H37rv
Organism_taxid: 83332
Strain: H37rv
Atcc: 25618
Gene: Rpoa
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petduet

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
Organism_scientific: Mycobacterium Tuberculosis H37rv
Organism_taxid: 83332
Strain: H37rv
Atcc: 25618
Gene: Rpob
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacycduet

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 H37rv
Organism_taxid: 83332
Strain: H37rv
Atcc: 25618
Gene: Rpoc
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacycduet

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 H37rv
Organism_taxid: 83332
Strain: H37rv
Atcc: 25618
Gene: Rpoz
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petduet

Molecule: Ecf Rna Polymerase Sigma Factor Sigh,Ecf Rna Poly Sigma Factor Sige,Ecf Rna Polymerase Sigma Factor Sigh;
Chain: F
Fragment: Unp Residues 1-95, Unp Residues 150-188, Unp Resi 216;
Synonym: Ecf Sigma Factor Sigh,Alternative Rna Polymerase S Factor Sigh,Rna Polymerase Sigma-H Factor,Sigma-H Factor,Ec Factor Sige,Alternative Rna Polymerase Sigma Factor Sige,Rn Polymerase Sigma-E Factor,Sigma-E Factor;
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37rv
Organism_taxid: 83332
Strain: H37rv
Gene: Sigh, Sige
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptolo-Ex5

Molecule: Dna (5'- D(Tptpgptpgpgpgpapgpcptpgptpcpapcpgpgpap A)-3');
Chain: G
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Tpgpcpaptpcpcpgptpgpapgptpcpgpapgpgpgp
Chain: H
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna (5'-R(Cpcpupcpgpa)-3')
Chain: I
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.195 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
128.943 163.005 129.315 90.00 117.81 90.00
method X-Ray Diffractionresolution 3.11 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


F


Primary referenceStructures and mechanism of transcription initiation by bacterial ECF factors., Fang C, Li L, Shen L, Shi J, Wang S, Feng Y, Zhang Y, Nucleic Acids Res. 2019 May 27. pii: 5498757. doi: 10.1093/nar/gkz470. PMID:31131408
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (505 Kb) [Save to disk]
  • Biological Unit Coordinates (6jcy.pdb1.gz) 496 Kb
  • LPC: Ligand-Protein Contacts for 6JCY
  • CSU: Contacts of Structural Units for 6JCY
  • Structure Factors (590 Kb)
  • Retrieve 6JCY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6JCY from S2C, [Save to disk]
    • View 6JCY 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 6JCY
  • 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: [6jcy_F] [6jcy_I] [6jcy_C] [6jcy_E] [6jcy_D] [6jcy_G] [6jcy_B] [6jcy_H] [6jcy_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6JCY
  • Community annotation for 6JCY at PDBWiki (http://pdbwiki.org)

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