3DCM

Crystal structure of the Thermotoga maritima SPOUT family RNA-methyltransferase protein Tm1570 in complex with S-adenosyl-L-methionine

PDB DOI: https://doi.org/10.2210/pdb3DCM/pdb

Classification: TRANSFERASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-04 Released: 2008-12-09
Deposition Author(s): Kim, D.J., Kim, H.S., Lee, S.J., Suh, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.235 (Depositor), 0.230 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Thermotoga maritima SPOUT superfamily RNA methyltransferase Tm1570 in complex with S-adenosyl-L-methionine

Kim, D.J., Kim, H.S., Lee, S.J., Suh, S.W.

(2009) Proteins 74: 245-249

PubMed: 18831037 Search on PubMed
DOI: https://doi.org/10.1002/prot.22249
Primary Citation of Related Structures:
3DCM

Organizational Affiliation

Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea.

Macromolecule Content

Total Structure Weight: 22.41 kDa
Atom Count: 1,670
Modelled Residue Count: 188
Deposited Residue Count: 192
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein TM_1570	A [auth X]	192	Thermotoga maritima	Mutation(s): 0 Gene Names: TM_1570
UniProt
Find proteins for Q9X1Q6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1Q6 Go to UniProtKB: Q9X1Q6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X1Q6
Sequence Annotations Expand
Reference Sequence LOADING

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 X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.235 (Depositor), 0.230 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.648	α = 90
b = 63.402	β = 129.03
c = 54.522	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
SOLVE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-12-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-12-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-03-20
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.