[English] 日本語
Yorodumi
- PDB-8hm5: Epoxide hydrolase from Caballeronia sordidicola PAMC 26510 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hm5
TitleEpoxide hydrolase from Caballeronia sordidicola PAMC 26510
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / Bacterial epoxide hydrolase
Function / homologyEpoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Epoxide hydrolase
Function and homology information
Biological speciesCaballeronia sordidicola (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsHwang, J. / Lee, M.J. / Do, H. / Lee, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)PM22030 Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural insights into the distinct substrate preferences of two bacterial epoxide hydrolases.
Authors: Hwang, J. / Lee, M.J. / Lee, S.G. / Do, H. / Lee, J.H.
History
DepositionDec 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Epoxide hydrolase
B: Epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)71,4122
Polymers71,4122
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-8 kcal/mol
Surface area23350 Å2
Unit cell
Length a, b, c (Å)43.470, 81.210, 79.830
Angle α, β, γ (deg.)90.000, 93.110, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Epoxide hydrolase


Mass: 35706.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caballeronia sordidicola (bacteria) / Gene: PAMC26510_32755 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A242M8J4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.03 Å3/Da / Density % sol: 39.43 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium formate and 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 5, 2020
RadiationMonochromator: Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.43→81.21 Å / Num. obs: 20365 / % possible obs: 97.7 % / Redundancy: 4.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.5
Reflection shellResolution: 2.43→2.56 Å / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 2022 / CC1/2: 0.968

-
Processing

Software
NameVersionClassification
REFMAC5.5refinement
PHENIX1.14_3260refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→43.41 Å / SU ML: 0.2255 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.5241 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2173 974 4.79 %
Rwork0.1705 19355 -
obs0.1728 20329 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.68 Å2
Refinement stepCycle: LAST / Resolution: 2.43→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4944 0 0 182 5126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115094
X-RAY DIFFRACTIONf_angle_d1.22416937
X-RAY DIFFRACTIONf_chiral_restr0.0791717
X-RAY DIFFRACTIONf_plane_restr0.0079910
X-RAY DIFFRACTIONf_dihedral_angle_d25.37571799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.560.2541230.19132673X-RAY DIFFRACTION93.98
2.56-2.720.23511230.19642730X-RAY DIFFRACTION96.78
2.72-2.930.28011200.20012765X-RAY DIFFRACTION97.4
2.93-3.230.2581130.20322765X-RAY DIFFRACTION97.46
3.23-3.70.25581550.17152807X-RAY DIFFRACTION98.47
3.7-4.650.17181590.13682788X-RAY DIFFRACTION98.76

+
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