5X22

Crystal structure of Thermus thermophilus transcription initiation complex with GpA and CMPcPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 5X22

Classification: TRANSFERASE / DNA

Total Structure Weight: 890215.69


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase subunit alpha A, B, K, L 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, M 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, N 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, O 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, P 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, Q 21 Thermus thermophilus
promoter DNA nontemplate strand H, R 27 Thermus thermophilus
RNA (5'-R(*GP*A)-3') I, S 2 Thermus thermophilus

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

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

B, D, F, L, N, P 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: 3.35 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.208
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 186.41 α = 90.00
b = 104.32 β = 98.36
c = 297.29 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

  • 2017-09-20
    Type: Author supporting evidence