1SMY

Structural basis for transcription regulation by alarmone ppGpp

Structural Biology Knowledgebase: 1SMY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.186

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1SMY

Classification: TRANSFERASE

Total Structure Weight: 862941.06

Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase alpha chain A, B, K, L 315 Thermus thermophilus EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase beta chain 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 beta' chain D, N 1524 Thermus thermophilus EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoC TTHA1812
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA POLYMERASE OMEGA SUBUNIT E, O 99 Thermus thermophilus EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoZ TTHA1561
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
principal sigma factor F, P 423 Thermus thermophilus Gene Name(s): sigA rpoD TT_C0164
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
G4P
Query on G4P

N GUANOSINE-5',3'-TETRAPHOSPHATE
C10 H17 N5 O17 P4
BUFLLCUFNHESEH-UUOKFMHZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A, B, C, D, E, F, M, N MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.186
  • Space Group: P 32

Unit Cell:

Length (Å) Angle (°)
a = 236.35 α = 90.00
b = 236.35 β = 90.00
c = 249.04 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-03-10
  • Released Date: 2004-05-18
  • Deposition author(s): Artsimovitch, I., Patlan, V., Sekine, S., Vassylyeva, M.N., Hosaka, T., Ochi, K., Yokoyama, S., Vassylyev, D.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4