4S2Y

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.172

Literature

Macromolecules
Sequence Display for 4S2Y

Classification: hydrolase / RNA

Total Structure Weight: 20263.81


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 3 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)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B 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: 1.6 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.172
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 79.63 α = 90.00
b = 36.48 β = 102.30
c = 58.07 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