3DOU | pdb_00003dou

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.195 (Depositor), 0.193 (DCC)
R-Value Work:
0.166 (Depositor), 0.164 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 (PDB Primary Data), 2.1.1.166 (UniProt)
UniProt
Find proteins for Q97C13 (Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)) Explore Q97C13 Go to UniProtKB: Q97C13
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97C13
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 1.45 Å
R-Value Free: 0.195 (Depositor), 0.193 (DCC)
R-Value Work: 0.166 (Depositor), 0.164 (DCC)
R-Value Observed: 0.167 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-09-02

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

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
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Structure summary