4G7Z Transcription, Transferase Dna date Jul 20, 2012
title Crystal Structure Of Thermus Thermophilus Transcription Init Complex Containing 5-Bru At Template-Strand Position +1
authors Y.Zhang, R.H.Ebright
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, K, L
Synonym: Rnap Subunit Alpha, Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C, M
Synonym: Rnap Subunit Beta, Rna Polymerase Subunit Beta, Transcriptase Subunit Beta;
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D, N
Synonym: Rna Polymerase Beta-Prime Subunit, Rnap Subunit Be Polymerase Subunit Beta', Transcriptase Subunit Beta';
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

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

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Rna Polymerase Sigma Factor
Chain: F, P
Synonym: Rna Polymerase Principle Sigma Factor, Sigma A
Engineered: Yes

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Rpod, Ttha0532
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: 5'-D(Tpaptpapaptpgpgpgpapgpcptpgpt Gpgpaptpgpcpapgpg)-3';
Chain: H, R
Engineered: Yes
Other_details: Nontemplate Strand

Synthetic: Yes

Molecule: 5'-D(Cpcptpgpcpaptpcpcpgptpgpapgp( Pcpgpapgpgpg)-3';
Chain: G, Q
Engineered: Yes
Other_details: Template Strand

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.176 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
185.465 103.590 296.507 90.00 98.53 90.00
method X-Ray Diffractionresolution 3.81 Å
ligand BRU, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, K, B, L


F, P
  • bacterial sigma factor activ...


  • M, C


    N, D


    O, E


    Primary referenceStructural Basis of Transcription Initiation., Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX, Arnold E, Ebright RH, Science. 2012 Oct 18. PMID:23086998
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1166 Kb) [Save to disk]
  • Biological Unit Coordinates (4g7z.pdb1.gz) 586 Kb
  • Biological Unit Coordinates (4g7z.pdb2.gz) 586 Kb
  • LPC: Ligand-Protein Contacts for 4G7Z
  • CSU: Contacts of Structural Units for 4G7Z
  • Structure Factors (549 Kb)
  • Retrieve 4G7Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4G7Z from S2C, [Save to disk]
  • Re-refined 4g7z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4G7Z 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 4G7Z
  • 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
  • 3D motif for 4G7Z, from MSDmotif at EBI
  • Fold representative 4g7z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4g7z_A] [4g7z_Q] [4g7z_M] [4g7z_B] [4g7z_K] [4g7z_N] [4g7z_L] [4g7z_E] [4g7z_C] [4g7z_F] [4g7z_D] [4g7z_G] [4g7z] [4g7z_R] [4g7z_O] [4g7z_H] [4g7z_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4G7Z: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4G7Z
  • Community annotation for 4G7Z at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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