[English] 日本語
Yorodumi
- PDB-8agp: Halogenated product of limonene epoxide turnover by epoxide hydro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8agp
TitleHalogenated product of limonene epoxide turnover by epoxide hydrolase from metagenomic source ch65
ComponentsAlpha/beta epoxide hydrolase
KeywordsHYDROLASE / Alpha/beta hydrolase fold / complex with substrate / limonene epoxide
Function / homologyEpoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Chem-M1U / Alpha/beta epoxide hydrolase
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsIsupov, M.N. / De Rose, S.A. / Mitchell, D. / Littlechild, J.A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)265933European Union
CitationJournal: To Be Published
Title: Complexes of epoxide hydrolase from metagenomic source ch65
Authors: Isupov, M.N. / De Rose, S.A. / Mitchell, D. / Littlechild, J.A. / Parker, E. / Ferrandi, E. / Guazzelli, E. / Monti, D.
History
DepositionJul 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Alpha/beta epoxide hydrolase
BBB: Alpha/beta epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,23119
Polymers69,8812
Non-polymers1,35017
Water7,782432
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.830, 46.110, 93.000
Angle α, β, γ (deg.)90.000, 98.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 4 - 289 / Label seq-ID: 4 - 289

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

-
Protein , 1 types, 2 molecules AAABBB

#1: Protein Alpha/beta epoxide hydrolase


Mass: 34940.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1U9WZ52

-
Non-polymers , 5 types, 449 molecules

#2: Chemical
ChemComp-M1U / (1~{S},2~{S},4~{R})-2-chloranyl-1-methyl-4-prop-1-en-2-yl-cyclohexan-1-ol


Mass: 188.694 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17ClO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 291 K / Method: microbatch
Details: Morpheus crystallisation kit condition C1; 40% v/v PEG 500* MME; 20% w/v PEG 20000. The crystal was incubated with 1mM mixture of cis (1R,2S,4R) and trans (1S,2R,4R) isomers of (+)-limonene ...Details: Morpheus crystallisation kit condition C1; 40% v/v PEG 500* MME; 20% w/v PEG 20000. The crystal was incubated with 1mM mixture of cis (1R,2S,4R) and trans (1S,2R,4R) isomers of (+)-limonene oxide for 1 hour 20 mins to produce a halogenated product in the active site.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.49→51.263 Å / Num. obs: 93810 / % possible obs: 99.1 % / Redundancy: 3.2 % / CC1/2: 0.998 / Net I/σ(I): 8.8
Reflection shellResolution: 1.49→1.52 Å / Num. unique obs: 4644 / CC1/2: 0.366

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
BUSTERrefinement
PARROTphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ng7

5ng7


Resolution: 1.49→51.263 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.108 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.083 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2156 4702 5.013 %
Rwork0.1779 89093 -
all0.18 --
obs-93795 99.067 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 26.938 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å2-0.937 Å2
2--0.014 Å2-0 Å2
3---1.123 Å2
Refinement stepCycle: LAST / Resolution: 1.49→51.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 0 79 432 5333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125393
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.6477372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9995682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28622.431288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.396151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7131530
X-RAY DIFFRACTIONr_chiral_restr0.1160.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024078
X-RAY DIFFRACTIONr_nbd_refined0.2250.22596
X-RAY DIFFRACTIONr_nbtor_refined0.3210.23624
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2369
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2560.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1990.236
X-RAY DIFFRACTIONr_mcbond_it4.626.1162440
X-RAY DIFFRACTIONr_mcangle_it5.68810.2433073
X-RAY DIFFRACTIONr_scbond_it7.0277.4142953
X-RAY DIFFRACTIONr_scangle_it8.75411.834246
X-RAY DIFFRACTIONr_lrange_it9.20745.7523136
X-RAY DIFFRACTIONr_ncsr_local_group_10.1230.059970
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.123280.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.123280.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.49-1.5290.3393350.32765840.32869870.5170.54399.02680.312
1.529-1.5710.3153090.31363860.31367380.6520.66399.36180.296
1.571-1.6160.3063410.28461710.28565630.7360.75399.22290.261
1.616-1.6660.3073360.27460410.27664280.8010.81199.20660.248
1.666-1.720.2753160.24758790.24862450.8440.85499.19940.218
1.72-1.7810.283030.22356240.22659750.8810.89499.19670.195
1.781-1.8480.2582910.20155060.20458200.8980.90899.60480.174
1.848-1.9230.2322600.1953170.19256060.9150.92899.48270.166
1.923-2.0080.2262880.18350450.18653530.9270.93799.62640.164
2.008-2.1060.2032720.16948280.17151220.9410.95699.57050.154
2.106-2.220.2282400.17546170.17848820.9320.94999.48790.162
2.22-2.3540.2122200.16943740.17146190.9370.95199.45880.157
2.354-2.5170.2122210.16141200.16443670.9430.95899.40460.152
2.517-2.7180.1871960.15538210.15740590.9580.96198.96530.15
2.718-2.9760.2071740.1635240.16237580.9510.96198.40340.158
2.976-3.3260.1961780.15931570.16134070.9560.96197.88670.161
3.326-3.8380.1721410.14128080.14330240.9660.97397.51980.154
3.838-4.6940.1621280.12523430.12725460.9690.97697.05420.144
4.694-6.6110.202940.1518670.15220070.9660.97597.7080.176
6.611-51.2630.207590.20310810.20311690.9590.96897.51920.246

+
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