5VO8

X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.185

Literature

Macromolecules
Sequence Display for 5VO8

Classification: transcription / DNA / RNA

Total Structure Weight: 444996.41


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 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(P*GP*GP*TP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*AP*AP*AP*A)-3') G 22 Bacillus subtilis
DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*CP*TP*GP*AP*TP*GP*CP*AP*CP*C)-3') H 27 Bacillus subtilis
RNA (5'-D(*(GTP))-R(P*GP*GP*GP*GP*GP*GP*G)-3') I 8 Thermus thermophilus

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

C PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
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

B, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
GTP
Query on GTP
I NON-POLYMER C10 H16 N5 O14 P3 G

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.185
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 186.54 α = 90.00
b = 101.98 β = 98.56
c = 296.11 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-05-02
  • Released Date: 2017-05-24
  • Deposition author(s): Murakami, K.S., Shin, Y., Turnbough Jr, C.L., Molodtsov, V.

Revision History

No revisions since initial release