4S2X

Structure of E. coli RppH bound to RNA and two magnesium ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.189

Literature

Macromolecules
Sequence Display for 4S2X

Classification: hydrolase / RNA

Total Structure Weight: 20300.12


Macromolecule Entities
Molecule Chains Length Organism Details
RNA pyrophosphohydrolase A 161 Escherichia coli EC#: 3.6.1 IUBMB
Mutation: Q160A, E161A
Gene Name(s): rppH nudH ygdP b2830 JW2798
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(*(APC)*GP*U)-3') B 3 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A 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
APC
Query on APC
B NON-POLYMER C11 H18 N5 O12 P3 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.189
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 78.50 α = 90.00
b = 38.87 β = 100.13
c = 57.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-01-23
  • Released Date: 2015-02-11
  • Deposition author(s): Vasilyev, N., Serganov, A.

Revision History

  • Version 1_0: 2015-02-11

    Type: Initial release

  • Version 1_1: 2015-02-25

    Type: Database references

  • Version 1_2: 2015-05-06

    Type: Database references