5VSW Transferase Dna date May 12, 2017
title X-Ray Crystal Structure Of Escherichia Coli Rna Polymerase A Dksappgpp Complex
authors K.S.Murakami, V.Molodtsov
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, G, H
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Engineered: Yes
Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Rpoa, Pez, Phs, Sez, B3295, Jw3257
Expression_system: Unidentified Plasmid
Expression_system_taxid: 45202

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C, I
Synonym: Rnap Subunit Beta,Rna Polymerase Subunit Beta,Tran Subunit Beta;
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Rpob, Gron, Nitb, Rif, Ron, Stl, Stv, Tabd, B3987, Jw
Expression_system: Unidentified Plasmid
Expression_system_taxid: 45202

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D, J
Synonym: Rnap Subunit Beta',Rna Polymerase Subunit Beta', Transcriptase Subunit Beta';
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Rpoc, Tabb, B3988, Jw3951
Expression_system: Unidentified Plasmid
Expression_system_taxid: 45202

Molecule: Dna-Directed Rna Polymerase Subunit Omega
Chain: E, K
Synonym: Rnap Omega Subunit,Rna Polymerase Omega Subunit, Transcriptase Subunit Omega;
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Rpoz, B3649, Jw3624
Expression_system: Unidentified Plasmid
Expression_system_taxid: 45202

Molecule: Rna Polymerase Sigma Factor Rpod
Chain: F, L
Synonym: Sigma-70
Engineered: Yes

Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Rpod, Alt, B3067, Jw3039
Expression_system: Unidentified Plasmid
Expression_system_taxid: 45202

Molecule: Rna Polymerase-Binding Transcription Factor Dksa
Chain: M
Synonym: Dnak Suppressor Protein
Engineered: Yes

Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Dksa, B0145, Jw0141
Expression_system: Unidentified Plasmid
Expression_system_taxid: 45202
symmetry Space Group: P 21 21 21
R_factor 0.221 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
187.274 205.259 311.313 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.30 Å
ligand
enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B, H, G


C, I


F, L
  • bacterial sigma factor activ...


  • J, D


    K, E


    M


    Primary referenceAllosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA., Molodtsov V, Sineva E, Zhang L, Huang X, Cashel M, Ades SE, Murakami KS, Mol Cell. 2018 Mar 1;69(5):828-839.e5. doi: 10.1016/j.molcel.2018.01.035. Epub, 2018 Feb 22. PMID:29478808
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2547 Kb) [Save to disk]
  • Biological Unit Coordinates (5vsw.pdb1.gz) 1329 Kb
  • Biological Unit Coordinates (5vsw.pdb2.gz) 1216 Kb
  • CSU: Contacts of Structural Units for 5VSW
  • Structure Factors (1953 Kb)
  • Retrieve 5VSW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VSW from S2C, [Save to disk]
  • Re-refined 5vsw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5VSW 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 5VSW
  • 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 5vsw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vsw_G] [5vsw_F] [5vsw_B] [5vsw_K] [5vsw_M] [5vsw_E] [5vsw_D] [5vsw_I] [5vsw_A] [5vsw_J] [5vsw_H] [5vsw_L] [5vsw_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VSW
  • Community annotation for 5VSW at PDBWiki (http://pdbwiki.org)

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