5TW1 Transcription Activator Transferase Dna date Nov 10, 2016
title Crystal Structure Of A Mycobacterium Smegmatis Transcription Initiation Complex With Rbpa
authors E.A.Hubin, 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, T
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
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: 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: Rpod, Siga, Msmeg_2758, Msmei_2690
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna (31-Mer)
Chain: O
Engineered: Yes
Synthetic: Yes
Organism_scientific: Aquifex Aeolicus
Organism_taxid: 63363

Molecule: Dna (26-Mer)
Chain: P
Engineered: Yes
Synthetic: Yes
Organism_scientific: Aquifex Aeolicus
Organism_taxid: 63363

Molecule: Unknown Peptide
Chain: G
Organism_scientific: Mycobacterium Smegmatis Str. Mc2 155
Organism_taxid: 246196
symmetry Space Group: P 1 21 1
R_factor 0.239 R_Free 0.280
crystal
cell
length a length b length c angle alpha angle beta angle gamma
133.012 161.633 139.211 90.00 107.72 90.00
method X-Ray Diffractionresolution 2.76 Å
ligand EDO, MG, SO4, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene MSMEG ; MSMEG ; MSMEI ; MSMEI
Gene
Ontology
ChainFunctionProcessComponent
A, T, B


C


D


E


F
  • bacterial sigma factor activ...


    • J


    Primary referenceStructure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA., Hubin EA, Fay A, Xu C, Bean JM, Saecker RM, Glickman MS, Darst SA, Campbell EA, Elife. 2017 Jan 9;6. pii: e22520. doi: 10.7554/eLife.22520. PMID:28067618
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (546 Kb) [Save to disk]
  • Biological Unit Coordinates (5tw1.pdb1.gz) 534 Kb
  • LPC: Ligand-Protein Contacts for 5TW1
  • CSU: Contacts of Structural Units for 5TW1
  • Structure Factors (3044 Kb)
  • Retrieve 5TW1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TW1 from S2C, [Save to disk]
  • Re-refined 5tw1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5TW1 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 5TW1
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5tw1_E] [5tw1_J] [5tw1_T] [5tw1_O] [5tw1_G] [5tw1_B] [5tw1] [5tw1_F] [5tw1_C] [5tw1_A] [5tw1_D] [5tw1_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5TW1
  • Community annotation for 5TW1 at PDBWiki (http://pdbwiki.org)

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