4CCL

X-Ray structure of E. coli ycfD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 4CCL

Classification: OXIDOREDUCTASE

Total Structure Weight: 87267.68

Macromolecule Entities
Molecule Chains Length Organism Details
50S RIBOSOMAL PROTEIN L16 ARGININE HYDROXYLASE A, B 373 Escherichia coli EC#: 1.14.11.47 IUBMB
Gene Name(s): roxA ycfD b1128 JW1114
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

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

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.198
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 120.69 α = 90.00
b = 120.69 β = 90.00
c = 133.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-10-23
  • Released Date: 2014-04-30
  • Deposition author(s): McDonough, M.A., Ho, C.H., Kershaw, N.J., Schofield, C.J.

Revision History

  • Version 1_0: 2014-04-30

    Type: Initial release

  • Version 1_1: 2014-05-14

    Type: Database references

  • Version 1_2: 2014-05-21

    Type: Database references

  • Version 1_3: 2014-06-25

    Type: Database references