4Q4Z

Thermus thermophilus RNA polymerase de novo transcription initiation complex

Structural Biology Knowledgebase: 4Q4Z SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.256

Literature

Macromolecules
Sequence Display for 4Q4Z

Classification: transcription / DNA

Total Structure Weight: 443008.03


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase subunit alpha A, B 315 Thermus thermophilus EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit beta C 1119 Thermus thermophilus EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoB TTHA1813
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit beta' D 1524 Thermus thermophilus EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoC TTHA1812
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit omega E 99 Thermus thermophilus EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoZ TTHA1561
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase sigma factor SigA F 423 Thermus thermophilus Gene Name(s): sigA TTHA0532
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
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') G 22 synthetic template DNA
DNA (25-MER) H 27 synthetic non-template DNA

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ATP
Query on ATP

C ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
2TM
Query on 2TM

D 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine
CMPcPP (Synonym)
C10 H18 N3 O13 P3
STGUOVSTMBLHFT-ZOQUXTDFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.256
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 184.49 α = 90.00
b = 102.16 β = 98.96
c = 294.72 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-04-15
  • Released Date: 2014-07-30
  • Deposition author(s): Murakami, K.S.

Revision History

  • 2014-10-08
    Type: Entry title | Details: --
  • 2014-09-24
    Type: Citation | Details: Citation update