5X21

Crystal structure of Thermus thermophilus transcription initiation complex with GpA and pseudouridimycin (PUM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.232

Literature

Macromolecules
Sequence Display for 5X21

Classification: TRANSFERASE / DNA

Total Structure Weight: 445097.09


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 TTHA1664
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 TT_C1196
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase sigma factor SigA F 443 Thermus thermophilus Gene Name(s): sigA rpoD TT_C0164
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
promoter DNA template strand G 21 Thermus thermophilus
promoter DNA nontemplate strand H 27 Thermus thermophilus
RNA (5'-R(*GP*A)-3') I 2 Thermus thermophilus

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

I (1S)-1,4-anhydro-5-[(N-carbamimidoylglycyl- N~2~-hydroxy-L-glutaminyl)amino]-5-deoxy- 1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin- 5-yl)-D-ribitol
pseudouridimycin (Synonym)
C17 H26 N8 O9
XDEYHXABZOKKDZ-YFKLLHAASA-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

A, C, D, F, H 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: 3.32 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.232
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 186.79 α = 90.00
b = 103.09 β = 98.71
c = 296.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-01-29
  • Released Date: 2017-07-05
  • Deposition author(s): Zhang, Y., Ebright, R.

Revision History

  • Version 1_0: 2017-07-05

    Type: Initial release