5X22 Transferase Dna date Jan 29, 2017
title Crystal Structure Of Thermus Thermophilus Transcription Init Complex With Gpa And Cmpcpp
authors Y.Zhang, R.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
Engineered: Yes
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
Gene: Rpoa
Expression_system: Thermus Thermophilus
Expression_system_taxid: 274

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C, M
Synonym: Rnap Subunit Beta,Rna Polymerase Subunit Beta,Tran Subunit Beta;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D, N
Synonym: Rnap Subunit Beta',Rna Polymerase Subunit Beta', Transcriptase Subunit Beta';
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

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 (Strain Hb27 At 163 Dsm 7039);
Organism_taxid: 262724
Strain: Hb27 Atcc Baa-163 Dsm 7039

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F, P
Engineered: Yes
Organism_scientific: Thermus Thermophilus (Strain Hb27 At 163 Dsm 7039);
Organism_taxid: 262724
Strain: Hb27 Atcc Baa-163 Dsm 7039
Gene: Siga, Rpod, Tt_c0164
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Promoter Dna Template Strand
Chain: G, Q
Engineered: Yes
Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Promoter Dna Nontemplate Strand
Chain: H, R
Engineered: Yes
Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Rna (5'-R(Gpa)-3')
Chain: I, S
Engineered: Yes
Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 1 21 1
R_factor 0.208 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
186.410 104.320 297.290 90.00 98.36 90.00
method X-Ray Diffractionresolution 3.35 Å
ligand
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 referenceAntibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase., Maffioli SI, Zhang Y, Degen D, Carzaniga T, Del Gatto G, Serina S, Monciardini P, Mazzetti C, Guglierame P, Candiani G, Chiriac AI, Facchetti G, Kaltofen P, Sahl HG, Deho G, Donadio S, Ebright RH, Cell. 2017 Jun 15;169(7):1240-1248.e23. doi: 10.1016/j.cell.2017.05.042. PMID:28622509
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1163 Kb) [Save to disk]
  • Biological Unit Coordinates (5x22.pdb1.gz) 578 Kb
  • Biological Unit Coordinates (5x22.pdb2.gz) 591 Kb
  • CSU: Contacts of Structural Units for 5X22
  • Structure Factors (2937 Kb)
  • Retrieve 5X22 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5X22 from S2C, [Save to disk]
  • Re-refined 5x22 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5X22 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 5X22
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5x22 from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5x22_S] [5x22_I] [5x22_G] [5x22_A] [5x22_B] [5x22_O] [5x22_K] [5x22_Q] [5x22_P] [5x22_D] [5x22_C] [5x22_N] [5x22_R] [5x22_F] [5x22_H] [5x22_L] [5x22_M] [5x22_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5X22
  • Community annotation for 5X22 at PDBWiki (http://pdbwiki.org)

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