[English] 日本語
Yorodumi
- PDB-25yv: Crystal structure of SchOMT2 from Schisandra chinensis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 25yv
TitleCrystal structure of SchOMT2 from Schisandra chinensis
ComponentsSchOMT2
KeywordsTRANSFERASE / O-methyltransferase / plant secondary metabolism / methyltransferase
Biological speciesSchisandra chinensis (Chinese magnolia-vine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsYang, G.H. / Yang, J.Z. / Xiong, R.L. / Xu, R.
Funding support China, United Kingdom, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U23A20511 China
National Natural Science Foundation of China (NSFC)82574540 China
CAMS Innovation Fund for Medical Sciences (CIFMS)2025-I2M-XHXX-114 United Kingdom
CitationJournal: To Be Published
Title: Enzymatic and structural basis of lignan methylation diversity in Schisandra chinensis accelerates the discovery of anticancer drug resistance reversers
Authors: Xiong, R.L. / Xu, R.
History
DepositionApr 23, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SchOMT2
B: SchOMT2


Theoretical massNumber of molelcules
Total (without water)83,6262
Polymers83,6262
Non-polymers00
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9380 Å2
ΔGint-70 kcal/mol
Surface area30790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.554, 57.657, 79.930
Angle α, β, γ (deg.)87.850, 74.080, 75.450
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein SchOMT2


Mass: 41812.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schisandra chinensis (Chinese magnolia-vine)
Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M KCl 0.05M HEPES pH7.1 35% Pentaerythritol propoxylate(5/4 PO/OH)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.67→76.82 Å / Num. obs: 79609 / % possible obs: 92.9 % / Redundancy: 2.9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.088 / Rrim(I) all: 0.124 / Net I/σ(I): 4.4
Reflection shellResolution: 1.67→1.71 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.674 / Num. unique obs: 10547 / CC1/2: 0.621 / % possible all: 84.1

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→21.46 Å / SU ML: 0.415 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.8765
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2864 3616 4.88 %
Rwork0.2355 70449 -
obs0.238 74065 86.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.63 Å2
Refinement stepCycle: LAST / Resolution: 1.67→21.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5418 0 0 303 5721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825528
X-RAY DIFFRACTIONf_angle_d0.98557456
X-RAY DIFFRACTIONf_chiral_restr0.058825
X-RAY DIFFRACTIONf_plane_restr0.0081957
X-RAY DIFFRACTIONf_dihedral_angle_d6.029734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.690.535480.4692834X-RAY DIFFRACTION26.82
1.69-1.720.4643740.49061211X-RAY DIFFRACTION39.15
1.72-1.740.4981140.47622143X-RAY DIFFRACTION68.52
1.74-1.770.5061160.45082087X-RAY DIFFRACTION66.62
1.77-1.790.43551090.43382445X-RAY DIFFRACTION78.15
1.79-1.820.45121390.39312762X-RAY DIFFRACTION87.46
1.82-1.860.35811570.36592803X-RAY DIFFRACTION88.97
1.86-1.890.37551170.35242849X-RAY DIFFRACTION91.74
1.89-1.930.39451360.34472907X-RAY DIFFRACTION91.49
1.93-1.960.34771490.31442946X-RAY DIFFRACTION94.24
1.96-2.010.34091590.28762942X-RAY DIFFRACTION94.66
2.01-2.050.32011660.27383028X-RAY DIFFRACTION95.89
2.05-2.110.39011650.29443001X-RAY DIFFRACTION95.77
2.11-2.160.30221570.24942991X-RAY DIFFRACTION97.07
2.16-2.230.33661310.2513130X-RAY DIFFRACTION97.11
2.23-2.30.2961480.27613001X-RAY DIFFRACTION96.77
2.3-2.380.33811490.25493068X-RAY DIFFRACTION97.28
2.38-2.470.34921600.24773052X-RAY DIFFRACTION97.54
2.47-2.590.31321760.25143030X-RAY DIFFRACTION97.74
2.59-2.720.27361700.23133026X-RAY DIFFRACTION97.62
2.72-2.890.33221700.24053076X-RAY DIFFRACTION97.8
2.89-3.120.28351400.23113091X-RAY DIFFRACTION98.24
3.12-3.390.27111300.20952788X-RAY DIFFRACTION98.05
3.45-3.920.22031010.18872159X-RAY DIFFRACTION72.69
3.92-4.930.22311590.15683079X-RAY DIFFRACTION97.62
4.93-21.460.20111760.18253000X-RAY DIFFRACTION96.83

+
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