5VSW

X-ray crystal structure of Escherichia coli RNA polymerase and DksA/ppGpp complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.221

Literature

Macromolecules
Sequence Display for 5VSW

Classification: transferase / dna

Total Structure Weight: 939553.56

Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase subunit alpha A, B, G, H 329 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoA pez phs sez b3295 JW3257
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit beta C, I 1342 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoB groN nitB rif ron stl stv tabD b3987 JW3950
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit beta' D, J 1407 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoC tabB b3988 JW3951
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit omega E, K 91 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoZ b3649 JW3624
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase sigma factor RpoD F, L 613 Escherichia coli Gene Name(s): rpoD alt b3067 JW3039
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase-binding transcription factor DksA M 151 Escherichia coli Gene Name(s): dksA b0145 JW0141
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

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

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

D, J 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: 4.3 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.221
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 187.27 α = 90.00
b = 205.26 β = 90.00
c = 311.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-05-12
  • Released Date: 2017-06-14
  • Deposition author(s): Murakami, K.S., Molodtsov, V.

Revision History

  • Version 1_0: 2017-06-14

    Type: Initial release

  • Version 1_1: 2017-08-23

    Type: Data collection

  • Version 1_2: 2017-09-20

    Type: Author supporting evidence