4EDV

The structure of the S. aureus DnaG RNA Polymerase Domain bound to pppGpp and Manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.167

Literature

Macromolecules
Sequence Display for 4EDV

Classification: transferase / transferase inhibitor

Total Structure Weight: 38645.61

Macromolecule Entities
Molecule Chains Length Organism Details
DNA primase A 329 Staphylococcus aureus EC#: 2.7.7 IUBMB
Fragment: unp residues 111-436
Gene Name(s): dnaG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0O2
Query on 0O2

A guanosine 5'-(tetrahydrogen triphosphate) 3'- (trihydrogen diphosphate)
C10 H18 N5 O20 P5
KCPMACXZAITQAX-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BEN
Query on BEN

A BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.167
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 151.33 α = 90.00
b = 151.33 β = 90.00
c = 38.69 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-27
  • Released Date: 2012-07-25
  • Deposition author(s): Rymer, R.U., Solorio, F.A., Chu, C., Corn, J.E., Wang, J.D., Berger, J.M.

Revision History

  • Version 1_0: 2012-07-25

    Type: Initial release

  • Version 1_1: 2013-07-10

    Type: Database references

  • Version 1_2: 2014-11-12

    Type: Structure summary