[English] 日本語
Yorodumi
- PDB-8k76: Crystal structure of S-adenosylmethionine-dependent methyltransfe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k76
TitleCrystal structure of S-adenosylmethionine-dependent methyltransferase from Fusobacterium nucleatum
ComponentsS-adenosylmethionine-dependent methyltransferase
KeywordsTRANSFERASE / methyltransferase
Function / homology: / Methyltransferase type 11 / Methyltransferase domain / S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Methyltransferase
Function and homology information
Biological speciesFusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.49 Å
AuthorsHe, S.R. / Bai, X. / Zhang, J. / Zhao, Z.D.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of S-adenosylmethionine-dependent methyltransferase from Fusobacterium nucleatum
Authors: He, S.R. / Bai, X.
History
DepositionJul 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-adenosylmethionine-dependent methyltransferase
B: S-adenosylmethionine-dependent methyltransferase


Theoretical massNumber of molelcules
Total (without water)57,2252
Polymers57,2252
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-17 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.981, 80.629, 108.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein S-adenosylmethionine-dependent methyltransferase


Mass: 28612.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Gene: FN1919 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q8R6D8, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG 3350,sodium citrate, ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.489→33 Å / Num. obs: 1036260 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.8
Reflection shellResolution: 1.49→1.52 Å / Num. unique obs: 42568 / CC1/2: 0.999

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.49→33 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 4436 4.89 %
Rwork0.214 --
obs0.2146 90737 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3663 0 0 158 3821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014
X-RAY DIFFRACTIONf_angle_d1.561
X-RAY DIFFRACTIONf_dihedral_angle_d6.236508
X-RAY DIFFRACTIONf_chiral_restr0.081578
X-RAY DIFFRACTIONf_plane_restr0.007662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.31441510.29792688X-RAY DIFFRACTION95
1.51-1.520.33971370.29232862X-RAY DIFFRACTION100
1.52-1.540.27661530.27442814X-RAY DIFFRACTION100
1.54-1.560.31791140.27282845X-RAY DIFFRACTION100
1.56-1.580.28231480.26272879X-RAY DIFFRACTION100
1.58-1.60.28341500.25182849X-RAY DIFFRACTION100
1.6-1.630.21511430.24012842X-RAY DIFFRACTION100
1.63-1.650.26571750.23792860X-RAY DIFFRACTION100
1.65-1.680.24041430.23152861X-RAY DIFFRACTION100
1.68-1.70.27381430.22022839X-RAY DIFFRACTION100
1.7-1.730.24871590.22152841X-RAY DIFFRACTION100
1.73-1.770.23141220.22832881X-RAY DIFFRACTION100
1.77-1.80.24861650.20942867X-RAY DIFFRACTION100
1.8-1.840.2461520.21632810X-RAY DIFFRACTION100
1.84-1.880.2131560.2062857X-RAY DIFFRACTION100
1.88-1.920.24581590.22042870X-RAY DIFFRACTION100
1.92-1.970.24571460.21912908X-RAY DIFFRACTION100
1.97-2.020.21231320.21242853X-RAY DIFFRACTION100
2.02-2.080.24381290.22142885X-RAY DIFFRACTION100
2.08-2.150.22481490.21732866X-RAY DIFFRACTION100
2.15-2.220.23091270.22432930X-RAY DIFFRACTION100
2.22-2.310.22341560.21032860X-RAY DIFFRACTION100
2.31-2.420.23611590.22142883X-RAY DIFFRACTION100
2.42-2.550.22341420.22932891X-RAY DIFFRACTION100
2.55-2.710.22851200.23412937X-RAY DIFFRACTION100
2.71-2.910.26331530.22882907X-RAY DIFFRACTION100
2.91-3.210.23951800.2342898X-RAY DIFFRACTION100
3.21-3.670.2181390.2052960X-RAY DIFFRACTION100
3.67-4.620.17741790.16912949X-RAY DIFFRACTION100
4.62-330.19081550.17793109X-RAY DIFFRACTION100

+
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