[English] 日本語
Yorodumi
- PDB-6fdf: Crystal structure of S. pombe Dnmt2 methyltransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fdf
TitleCrystal structure of S. pombe Dnmt2 methyltransferase
ComponentstRNA (cytosine(38)-C(5))-methyltransferase
KeywordsTRANSFERASE / Dnmt2 / Methyltransferase / S-adenosylhomocysteine / tRNA
Function / homology
Function and homology information


tRNA (cytidine) methyltransferase activity / tRNA (cytosine38-C5)-methyltransferase / tRNA C5-cytosine methylation / tRNA (cytidine-5-)-methyltransferase activity / tRNA binding / nucleus / cytosol
Similarity search - Function
: / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (cytosine(38)-C(5))-methyltransferase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.697 Å
AuthorsJohannsson, S. / Neumann, P. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSPP1784 Germany
CitationJournal: Sci Rep / Year: 2018
Title: Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine.
Authors: Johannsson, S. / Neumann, P. / Wulf, A. / Welp, L.M. / Gerber, H.D. / Krull, M. / Diederichsen, U. / Urlaub, H. / Ficner, R.
History
DepositionDec 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA (cytosine(38)-C(5))-methyltransferase
B: tRNA (cytosine(38)-C(5))-methyltransferase
C: tRNA (cytosine(38)-C(5))-methyltransferase
D: tRNA (cytosine(38)-C(5))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,75319
Polymers153,2034
Non-polymers2,55115
Water14,988832
1
A: tRNA (cytosine(38)-C(5))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0536
Polymers38,3011
Non-polymers7535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA (cytosine(38)-C(5))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9615
Polymers38,3011
Non-polymers6614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: tRNA (cytosine(38)-C(5))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8694
Polymers38,3011
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: tRNA (cytosine(38)-C(5))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8694
Polymers38,3011
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.817, 114.781, 113.759
Angle α, β, γ (deg.)90.000, 131.050, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
tRNA (cytosine(38)-C(5))-methyltransferase / DNA (cytosine-5)-methyltransferase-like protein 2 / Dnmt2 / M.SpomI / SpIM.SpoI


Mass: 38300.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: pmt1, SPBC19C2.02 / Production host: Escherichia coli (E. coli)
References: UniProt: P40999, tRNA (cytosine38-C5)-methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 50 mM MES pH 6.5 1 % w/v PEG 4000 4 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.697→40.795 Å / Num. obs: 162497 / % possible obs: 99 % / Redundancy: 3.492 % / Biso Wilson estimate: 33.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.035 / Χ2: 1.051 / Net I/σ(I): 20.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.83.5740.5092.69255330.8130.59899.3
1.8-1.93.5050.2684.86204180.9310.31799.4
1.9-23.3290.1488.18165900.9750.17699.1
2-2.53.5420.05918.68485820.9960.06999.2
2.5-33.5590.03233.28215440.9980.03899
3-43.3270.02443.18170270.9990.02998.3
4-53.5370.02255.3560930.9980.02698.7
5-63.3870.02255.5127350.9980.02698.3
6-103.2930.02552.7729040.9970.0397.4
10-203.3480.03151.897180.9940.03895.2
20-302.8570.03942.92700.990.04988.6
30-40.7952.1880.02932.9160.9960.03941

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.697→40.795 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.57
RfactorNum. reflection% reflection
Rfree0.1948 2099 1.29 %
Rwork0.1739 --
obs0.1742 162497 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.23 Å2 / Biso mean: 44.8102 Å2 / Biso min: 20.61 Å2
Refinement stepCycle: final / Resolution: 1.697→40.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10266 0 170 832 11268
Biso mean--51.43 49.64 -
Num. residues----1269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.697-1.73650.27721320.2706101051023794
1.7365-1.77990.25561420.24941080110943100
1.7799-1.8280.27381390.2381063210771100
1.828-1.88180.28971410.22841078710928100
1.8818-1.94260.2391400.2051106871082799
1.9426-2.0120.22911400.198107191085999
2.012-2.09250.22281410.19241074410885100
2.0925-2.18780.21231400.19391074110881100
2.1878-2.30310.23991410.19181072410865100
2.3031-2.44740.19341410.184107571089899
2.4474-2.63630.23181390.1854106891082899
2.6363-2.90160.21971410.1795107521089399
2.9016-3.32120.19041410.1759107391088099
3.3212-4.18380.15741400.1505106971083799
4.1838-40.80690.17211410.1564108241096599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.20450.16771.65520.75180.01871.57470.02060.1172-0.1506-0.0480.0544-0.01040.0967-0.0624-0.07990.3035-0.01570.02120.2513-0.04390.2395-41.793415.549197.3639
21.9955-0.309-0.99390.9843-0.12653.33830.05940.06530.0717-0.02450.0106-0.0398-0.00430.1284-0.06960.1837-0.0238-0.00220.1651-0.0210.2228-48.177543.655982.1556
31.5383-0.6967-0.80952.60731.03152.45310.0748-0.0510.14970.07420.0551-0.2427-0.29150.138-0.12470.2501-0.0346-0.02210.223-0.0290.2202-62.373113.052945.2919
43.1573-1.24971.66952.0932-0.79292.3324-0.1019-0.09980.03170.07260.0540.0483-0.1806-0.20.04330.2548-0.03050.01510.265-0.01740.2228-78.4336-16.362555.6275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 335)A6 - 335
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 335)B5 - 335
3X-RAY DIFFRACTION3(chain 'C' and resid 6 through 335)C6 - 335
4X-RAY DIFFRACTION4(chain 'D' and resid 6 through 335)D6 - 335

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more