3DOU

Crystal structure of methyltransferase involved in cell division from thermoplasma volcanicum gss1

• PDB DOI: https://doi.org/10.2210/pdb3DOU/pdb

• Classification: TRANSFERASE
• Organism(s): Thermoplasma volcanium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-06 Released: 2008-09-02 
• Deposition Author(s): Patskovsky, Y., Ozyurt, S., Dickey, M., Hu, S., Bain, K., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.195 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

Literature

Crystal Structure of Methyltransferase Involved in Cell Division from Thermoplasma Volcanicum

Patskovsky, Y., Ozyurt, S., Dickey, M., Hu, S., Bain, K., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.5 kDa 
• Atom Count: 1,668 
• Modelled Residue Count: 175 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal RNA large subunit methyltransferase J	A	191	Thermoplasma volcanium	Mutation(s): 0  Gene Names: rrmJ, TV0292, TVG0303954 EC: 2.1.1
UniProt
Find proteins for Q97C13 (Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)) Explore Q97C13  Go to UniProtKB:  Q97C13

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.195 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.62	α = 90
b = 50.053	β = 108.08
c = 56.457	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Patskovsky, Y., Ozyurt, S., Dickey, M., Hu, S., Bain, K., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary