[English] 日本語
Yorodumi
- PDB-8zsa: Crystal structure of 4VPMT2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zsa
TitleCrystal structure of 4VPMT2
Components4VPMT2
KeywordsTRANSFERASE / methyltransferase / 4-vinylanisole biosynthesis
Function / homology4-ethenylphenol / S-ADENOSYLMETHIONINE
Function and homology information
Biological speciesLocusta migratoria (migratory locust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsGao, L. / Yang, J. / Lei, X.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22193073 and 92253305 China
CitationJournal: Nature / Year: 2025
Title: Decoding 4-vinylanisole biosynthesis and pivotal enzymes in locusts.
Authors: Guo, X. / Gao, L. / Li, S. / Gao, J. / Wang, Y. / Lv, J. / Wei, J. / Yang, J. / Ke, H. / Ding, Q. / Yang, J. / Guo, F. / Zhang, H. / Lei, X. / Kang, L.
History
DepositionJun 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 9, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Aug 27, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4VPMT2
B: 4VPMT2
C: 4VPMT2
D: 4VPMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,5389
Polymers147,8254
Non-polymers1,7145
Water64936
1
A: 4VPMT2
C: 4VPMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8295
Polymers73,9122
Non-polymers9173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-16 kcal/mol
Surface area22410 Å2
MethodPISA
2
B: 4VPMT2
D: 4VPMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7094
Polymers73,9122
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-13 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.525, 101.525, 326.778
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein
4VPMT2


Mass: 36956.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Locusta migratoria (migratory locust) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-4VP / 4-ethenylphenol


Mass: 120.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 MMT buffer, 25% PEG1500, pH7.0-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 38865 / % possible obs: 98.8 % / Redundancy: 11.9 % / CC1/2: 0.955 / Rrim(I) all: 0.36 / Net I/σ(I): 10.5
Reflection shellResolution: 3.4→3.46 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1303 / CC1/2: 0.629 / % possible all: 87.9

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.42→29.62 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 3144 8.09 %
Rwork0.2124 --
obs0.2152 38865 76.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.42→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8811 0 117 36 8964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029168
X-RAY DIFFRACTIONf_angle_d0.5212498
X-RAY DIFFRACTIONf_dihedral_angle_d5.8531231
X-RAY DIFFRACTIONf_chiral_restr0.0411393
X-RAY DIFFRACTIONf_plane_restr0.0051608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.42-3.470.3115450.3069523X-RAY DIFFRACTION25
3.47-3.530.3777700.3309753X-RAY DIFFRACTION35
3.53-3.590.3217850.2909967X-RAY DIFFRACTION46
3.59-3.650.3928970.31131083X-RAY DIFFRACTION52
3.65-3.720.3151050.29781144X-RAY DIFFRACTION53
3.72-3.80.29581080.27461171X-RAY DIFFRACTION56
3.8-3.880.30851040.26251231X-RAY DIFFRACTION57
3.88-3.970.30881130.24711276X-RAY DIFFRACTION61
3.97-4.070.28781310.22151478X-RAY DIFFRACTION67
4.07-4.180.22691330.21241546X-RAY DIFFRACTION73
4.18-4.30.25581350.20961651X-RAY DIFFRACTION78
4.3-4.440.21671640.19571878X-RAY DIFFRACTION87
4.44-4.60.23381830.19672000X-RAY DIFFRACTION93
4.6-4.780.20631720.20342006X-RAY DIFFRACTION96
4.78-50.21311950.20562116X-RAY DIFFRACTION99
5-5.260.31661860.21522129X-RAY DIFFRACTION100
5.26-5.590.23271870.2132149X-RAY DIFFRACTION100
5.59-6.020.27971980.2282103X-RAY DIFFRACTION100
6.02-6.610.26291960.22322134X-RAY DIFFRACTION100
6.62-7.550.21411820.19912115X-RAY DIFFRACTION100
7.56-9.470.20231760.15862143X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 2.3352 Å / Origin y: 2.0404 Å / Origin z: 8.2938 Å
111213212223313233
T0.4775 Å20.1134 Å20.0823 Å2-0.2977 Å2-0.0104 Å2--0.2852 Å2
L0.6833 °2-0.086 °2-0.1107 °2-0.8657 °2-0.2704 °2--1.0009 °2
S-0.1339 Å °0.1324 Å °-0.0447 Å °0.0455 Å °-0.1826 Å °-0.059 Å °0.1747 Å °-0.1083 Å °0.2274 Å °
Refinement TLS groupSelection details: all

+
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