Thermus thermophilus RNA polymerase de novo transcription initiation complex
DOI:10.2210/pdb4q4z/pdb   NDB ID: NA2980
4Q4Z
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transcription/dna
    Structure Weight: 443007.93
    Molecule: DNA-directed RNA polymerase subunit alpha
    Polymer: 1 Type: protein Length: 315
    Chains: A, B
    EC#: 2.7.7.6   
    Organism: Thermus thermophilus
    Gene Name: rpoA
    UniProtKB: Search PDB | Q9Z9H6   Protein Feature View
    Molecule: DNA-directed RNA polymerase subunit beta
    Polymer: 2 Type: protein Length: 1119
    Chains: C
    EC#: 2.7.7.6   
    Organism: Thermus thermophilus HB8
    Gene Names: rpoB TTHA1813
    UniProtKB: Search PDB | Q8RQE9   Protein Feature View
    Molecule: DNA-directed RNA polymerase subunit beta'
    Polymer: 3 Type: protein Length: 1524
    Chains: D
    EC#: 2.7.7.6   
    Organism: Thermus thermophilus HB8
    Gene Names: rpoC TTHA1812
    UniProtKB: Search PDB | Q8RQE8   Protein Feature View
    Molecule: DNA-directed RNA polymerase subunit omega
    Polymer: 4 Type: protein Length: 99
    Chains: E
    EC#: 2.7.7.6   
    Organism: Thermus thermophilus HB8
    Gene Names: rpoZ TTHA1561
    UniProtKB: Search PDB | Q8RQE7   Protein Feature View
    Molecule: RNA polymerase sigma factor SigA
    Polymer: 5 Type: protein Length: 423
    Chains: F
    Organism: Thermus thermophilus HB8
    Gene Names: sigA TTHA0532
    UniProtKB: Search PDB | Q5SKW1   Protein Feature View
    Molecule: DNA (5'-D(*CP*CP*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*GP*CP*AP*GP*CP*CP*A)-3')
    Polymer: 6 Type: dna Length: 22
    Chains: G
    Details: template DNA
    Molecule: DNA (25-MER)
    Polymer: 7 Type: dna Length: 27
    Chains: H
    Details: non-template DNA
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 2
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 3
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 4
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 5
    Scientific Name: Thermus thermophilus   Taxonomy   Expression System: Escherichia coli  
    Polymer: 6
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 7
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    4Q5A    
    4Q5S    
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    2TM
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    2TM C10 H18 N3 O13 P3
    5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine
    ATP
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    ATP C10 H16 N5 O13 P3
    ADENOSINE-5'-TRIPHOSPHATE
    MG
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    MG Mg
    MAGNESIUM ION
    ZN
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    ZN Zn
    ZINC ION
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:NA2980
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Murakami, K.S.

    Deposition:   2014-04-15
    Release:   2014-07-30
    Last Modified (REVDAT):   2014-10-08
     
  •   Revision History    Hide
    Mouse over text for details
    2014-10-08
    Entry title
    2014-09-24
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   2.90
    R-Value: 0.256 (obs.)
    R-Free: 0.275
    Space Group: C 1 2 1
    Unit Cell:
      Length [Å] Angles [°]
    a = 184.49 α = 90.00 
    b = 102.16 β = 98.96 
    c = 294.72 γ = 90.00