6PMJ Transcription date Jul 02, 2019
title Sigm28-Transcription Initiation Complex With Specific Promot State 2
authors B.Liu, W.Shi
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: Escherichia Coli O157:H7
Organism_taxid: 83334
Gene: Rpoa, Z4665, Ecs4160
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
Organism_scientific: Escherichia Coli O45:K1 (Strain S88
Organism_taxid: 585035
Strain: S88 Expec
Gene: Rpob, Ecs88_4448
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: Escherichia Coli O157:H7
Organism_taxid: 83334
Gene: Rpoc, Z5561, Ecs4911
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: Escherichia Coli O45:K1 (Strain S88
Organism_taxid: 585035
Strain: S88 Expec
Gene: Rpoz, Ecs88_4064
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna Polymerase Sigma Factor Flia
Chain: F
Synonym: Rna Polymerase Sigma Factor For Flagellar Operon,S Sigma-27,Sigma-28;
Engineered: Yes
Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Flia, Flad, Rpof, B1922, Jw1907
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Synthetic Nontemplate Strand Dna (54-Mer)
Chain: 1
Engineered: Yes
Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Synthetic Template Strand Dna (54-Mer)
Chain: 2
Engineered: Yes
Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Nascent Rna
Chain: 3
Engineered: Yes
Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
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 3.91 Å
ligand ATP, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


F
  • bacterial sigma factor activ...


    • Primary referenceStructural basis of bacterial sigma(28) -mediated transcription reveals roles of the RNA polymerase zinc-binding domain., Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B, EMBO J. 2020 Jun 2:e104389. doi: 10.15252/embj.2020104389. PMID:32484956
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (962 Kb) [Save to disk]
  • Biological Unit Coordinates (6pmj.pdb1.gz) 955 Kb
  • LPC: Ligand-Protein Contacts for 6PMJ
  • CSU: Contacts of Structural Units for 6PMJ
  • Retrieve 6PMJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6PMJ from S2C, [Save to disk]
    • View 6PMJ 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 6PMJ
  • 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: [6pmj_C] [6pmj_3] [6pmj_D] [6pmj_A] [6pmj_B] [6pmj_2] [6pmj_F] [6pmj_1] [6pmj_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6PMJ
  • Community annotation for 6PMJ at PDBWiki (http://pdbwiki.org)

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