3EGV

Ribosomal protein L11 methyltransferase (PrmA) in complex with trimethylated ribosomal protein L11

Structural Biology Knowledgebase: 3EGV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.183

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3EGV

Classification: TRANSFERASE / RIBOSOMAL PROTEIN

Total Structure Weight: 44106.41

Macromolecule Entities
Molecule Chains Length Organism Details
Ribosomal protein L11 methyltransferase A 254 Thermus thermophilus EC#: 2.1.1 IUBMB
Gene Name(s): prmA TTHA0656
50S ribosomal protein L11 B 146 Thermus thermophilus Mutation: K16A
Gene Name(s): rplK TTHA0247

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SAH
Query on SAH

A S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
4MM
Query on 4MM

B (1S)-1-carboxy-N,N,N-trimethyl-3-(methylsulfanyl)propan- 1-aminium
C8 H18 N O2 S
LIOVZIQCHLSVBO-ZETCQYMHSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IOD
Query on IOD

B IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.183
  • Space Group: P 62
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 134.55 α = 90.00
b = 134.55 β = 90.00
c = 48.94 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-11
  • Released Date: 2008-09-23
  • Deposition author(s): Demirci, H., Gregory, S.T., Dahlberg, A.E., Jogl, G.
  • Previous versions: 3CJU

Revision History

  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor