1UWV

CRYSTAL STRUCTURE OF RUMA, THE IRON-SULFUR CLUSTER CONTAINING E. COLI 23S RIBOSOMAL RNA 5-METHYLURIDINE METHYLTRANSFERASE

Structural Biology Knowledgebase: 1UWV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.186

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1UWV

Classification: TRANSFERASE

Total Structure Weight: 49276.85

Macromolecule Entities
Molecule Chains Length Organism Details
23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA A 433 Escherichia coli EC#: 2.1.1.190 IUBMB
Details: IRON-SULFUR CLUSTER LINKED BY CYS81, CYS87, CYS90, AND CYS162
Gene Name(s): rlmD rumA ygcA b2785 JW2756

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SF4
Query on SF4

A IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.186
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 35.94 α = 90.00
b = 99.45 β = 100.57
c = 58.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-02-11
  • Released Date: 2004-03-18
  • Deposition author(s): Lee, T.T., Agarwalla, S., Stroud, R.M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4