[English] 日本語
Yorodumi
- PDB-8qwi: Comparison of room-temperature and cryogenic structures of solubl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qwi
TitleComparison of room-temperature and cryogenic structures of soluble Epoxide Hydrolase with ligands bound.
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / Inhibitor / serial crystallography / drug discovery / fixed target / room temperature / microcrystals
Function / homology
Function and homology information


lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / Biosynthesis of maresins / epoxide metabolic process / lysophosphatidic acid phosphatase activity / soluble epoxide hydrolase / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) ...lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / Biosynthesis of maresins / epoxide metabolic process / lysophosphatidic acid phosphatase activity / soluble epoxide hydrolase / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / dephosphorylation / regulation of cholesterol metabolic process / phosphatase activity / peroxisomal matrix / toxic substance binding / Peroxisomal protein import / cholesterol homeostasis / regulation of cell growth / response to toxic substance / peroxisome / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / extracellular exosome / cytosol
Similarity search - Function
Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / alpha/beta hydrolase fold / haloacid dehalogenase-like hydrolase / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
2-(1H-BENZIMIDAZOL-2-YLSULFANYL)ETHANOL / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsDunge, A. / Uwangue, O. / Phan, C. / Bjelcic, M. / Gunnarsson, J. / Wehlander, G. / Kack, H. / Branden, G.
Funding support Sweden, 4items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic ResearchID17-0060 Sweden
Swedish Research Council2017-06734 Sweden
Swedish Research Council2021-05662 Sweden
Swedish Research Council2021-05981 Sweden
CitationJournal: Iucrj / Year: 2024
Title: Exploring serial crystallography for drug discovery.
Authors: Dunge, A. / Phan, C. / Uwangue, O. / Bjelcic, M. / Gunnarsson, J. / Wehlander, G. / Kack, H. / Branden, G.
History
DepositionOct 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2933
Polymers62,0031
Non-polymers2902
Water3,765209
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,5866
Polymers124,0052
Non-polymers5814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area4660 Å2
ΔGint-44 kcal/mol
Surface area42620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.95, 93.95, 246.69
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Bifunctional epoxide hydrolase 2


Mass: 62002.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P34913
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-6N4 / 2-(1H-BENZIMIDAZOL-2-YLSULFANYL)ETHANOL


Mass: 194.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 32-42% PEG 3350, 0.1M Li2SO4 and 0.1M Tris-HCl (pH 8.2)

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.12→49.15 Å / Num. obs: 69231 / % possible obs: 100 % / Redundancy: 1116 % / CC1/2: 0.9929 / Net I/σ(I): 9.42
Reflection shellResolution: 2.12→2.13 Å / Num. unique obs: 2336 / CC1/2: 0.77
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→49.15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.193 / SU Rfree Blow DPI: 0.154 / SU Rfree Cruickshank DPI: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 1913 -RANDOM
Rwork0.1768 ---
obs0.1782 37504 100 %-
Displacement parametersBiso mean: 43.42 Å2
Baniso -1Baniso -2Baniso -3
1--3.3716 Å20 Å20 Å2
2---3.3716 Å20 Å2
3---6.7431 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.12→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4313 0 18 209 4540
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084477HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.926075HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1563SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes754HARMONIC5
X-RAY DIFFRACTIONt_it4477HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion567SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3608SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion16.26
LS refinement shellResolution: 2.12→2.13 Å
RfactorNum. reflection% reflection
Rfree0.311 38 -
Rwork0.2566 --
obs0.2591 751 100 %

+
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