2BH2

CRYSTAL STRUCTURE OF E. COLI 5-METHYLURIDINE METHYLTRANSFERASE RUMA IN COMPLEX WITH RIBOSOMAL RNA SUBSTRATE AND S-ADENOSYLHOMOCYSTEINE.

Structural Biology Knowledgebase: 2BH2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.174

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2BH2

Classification: TRANSFERASE

Total Structure Weight: 121465.65


Macromolecule Entities
Molecule Chains Length Organism Details
23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA A, B 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
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
23S RIBOSOMAL RNA 1932-1968 C, D 37 Escherichia coli 5-FLUORO-U1939 IS METHYLATED AND ITS 6-C IS COVALENTLY LINKED TO CYS389 OF RUMA

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

A, B S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

A, B IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
FMU
Query on FMU
C, D RNA LINKING C10 H16 F N2 O9 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.174
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 190.06 α = 90.00
b = 63.54 β = 125.15
c = 112.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-06
  • Released Date: 2005-03-30
  • 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