[English] 日本語
Yorodumi
- PDB-6ies: Onion lachrymatory factor synthase (LFS) containing (E)-2-propen ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ies
TitleOnion lachrymatory factor synthase (LFS) containing (E)-2-propen 1-ol (crotyl alcohol)
ComponentsLachrymatory-factor synthase
KeywordsISOMERASE / SRPBCC / helix-grip fold / cytosolic
Function / homologylachrymatory-factor synthase / : / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / vacuole / START-like domain superfamily / isomerase activity / (2E)-but-2-en-1-ol / Lachrymatory-factor synthase
Function and homology information
Biological speciesAllium cepa (onion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSato, Y. / Arakawa, T. / Takabe, J. / Masamura, N. / Tsuge, N. / Imai, S. / Fushinobu, S.
CitationJournal: Acs Catalysis / Year: 2020
Title: Dissecting the Stereocontrolled Conversion of Short-Lived Sulfenic Acid by Lachrymatory Factor Synthase.
Authors: Arakawa, T. / Sato, Y. / Yamada, M. / Takabe, J. / Yoshitaka Moriwaki, Y. / Masamura, N. / Kato, M. / Aoyagi, M. / Kamoi, T. / Terada, T. / Shimizu, K. / Tsuge, N. / Imai, S. / Fushinobu, S.
History
DepositionSep 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lachrymatory-factor synthase
B: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9554
Polymers39,8112
Non-polymers1442
Water2,900161
1
A: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9782
Polymers19,9061
Non-polymers721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9782
Polymers19,9061
Non-polymers721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.090, 50.090, 141.397
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Lachrymatory-factor synthase


Mass: 19905.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allium cepa (onion) / Gene: LFS / Production host: Escherichia coli (E. coli) / References: UniProt: P59082
#2: Chemical ChemComp-9A7 / (2E)-but-2-en-1-ol


Mass: 72.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG6000, 0.1 M MES-Na

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Feb 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 32193 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 28.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.53 / Num. unique obs: 1565 / CC1/2: 0.9 / Rsym value: 0.53 / % possible all: 100

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GTE

5gte


Resolution: 1.8→31.69 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.511 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.111
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 1559 4.9 %RANDOM
Rwork0.1787 ---
obs0.18 30579 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.87 Å2 / Biso mean: 28.869 Å2 / Biso min: 16.58 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.8→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 10 161 2601
Biso mean--31.11 32.37 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0152502
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172246
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.7293380
X-RAY DIFFRACTIONr_angle_other_deg0.5631.7225254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2735300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14922.43982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62315366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.198154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
LS refinement shellResolution: 1.799→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 110 -
Rwork0.223 2233 -
all-2343 -
obs--98.82 %

+
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