[English] 日本語
Yorodumi
- PDB-9c2g: ISOBUTYLENE EPOXIDE HYDROLASE FROM MYCOLICIBACTERIUM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9c2g
TitleISOBUTYLENE EPOXIDE HYDROLASE FROM MYCOLICIBACTERIUM
ComponentsIsobutylene epoxide hydrolase
KeywordsHYDROLASE / bacterial epoxide hydrolase / 2-methylpropene (isobutylene) / alpha/beta hydrolase fold / soluble epoxide hydrolase
Function / homologyOctadecane
Function and homology information
Biological speciesMycolicibacterium (Mycobacterium fortuitum complex)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsRose, R.B. / Swartz, P. / Faulkner, N.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentUS Department of Agriculture's National Institute of Food and Agriculture, Hatch Project NC02591, NCSU Biotechnology Program United States
CitationJournal: Appl.Environ.Microbiol. / Year: 2025
Title: Characterization of an isobutylene epoxide hydrolase (IbcK) from the isobutylene-catabolizing bacterium Mycolicibacterium sp. ELW1.
Authors: Faulkner, N.W. / Joyce, J.B. / Smith, C. / Swartz, P. / Rose, R.B. / Miller, E.S. / Hyman, M.R.
History
DepositionMay 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isobutylene epoxide hydrolase
B: Isobutylene epoxide hydrolase
C: Isobutylene epoxide hydrolase
D: Isobutylene epoxide hydrolase
E: Isobutylene epoxide hydrolase
F: Isobutylene epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,41223
Polymers220,9996
Non-polymers2,41217
Water4,972276
1
A: Isobutylene epoxide hydrolase
B: Isobutylene epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3847
Polymers73,6662
Non-polymers7175
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-37 kcal/mol
Surface area20120 Å2
MethodPISA
2
D: Isobutylene epoxide hydrolase
hetero molecules

C: Isobutylene epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5729
Polymers73,6662
Non-polymers9067
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_355-x-2,y+1/2,-z+1/21
Buried area3090 Å2
ΔGint-47 kcal/mol
Surface area20240 Å2
MethodPISA
3
E: Isobutylene epoxide hydrolase
F: Isobutylene epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4567
Polymers73,6662
Non-polymers7895
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-44 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.417, 181.005, 221.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Isobutylene epoxide hydrolase


Mass: 36833.191 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Environmental isolate from stream adjacent soil, Raleigh, NC, USA
Source: (gene. exp.) Mycolicibacterium (Mycobacterium fortuitum complex)
Strain: ELW1 / Gene: ibcK / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: EC: 3.3.23.10

-
Non-polymers , 5 types, 293 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical
ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H38
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M MgSO4, 0.1 M MES:NaOH / Temp details: l

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen gas / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→47.3 Å / Num. obs: 81304 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 37.98 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.049 / Rrim(I) all: 0.122 / Χ2: 1.2 / Net I/σ(I): 5.8
Reflection shellResolution: 2.29→2.34 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.634 / Num. unique obs: 3614 / CC1/2: 0.768 / CC star: 0.932 / Rpim(I) all: 0.311 / Rrim(I) all: 0.709 / % possible all: 83.5

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→47.3 Å / SU ML: 0.2599 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.9039
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 1990 2.46 %Random selection
Rwork0.1776 78746 --
obs0.1788 80736 90.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.76 Å2
Refinement stepCycle: LAST / Resolution: 2.29→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14100 0 109 276 14485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002714637
X-RAY DIFFRACTIONf_angle_d0.567119936
X-RAY DIFFRACTIONf_chiral_restr0.04312114
X-RAY DIFFRACTIONf_plane_restr0.00532563
X-RAY DIFFRACTIONf_dihedral_angle_d13.75915131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.29221190.22474791X-RAY DIFFRACTION78.62
2.35-2.410.22551320.22245200X-RAY DIFFRACTION84.47
2.41-2.480.29611310.21865173X-RAY DIFFRACTION85.26
2.48-2.560.31391350.22245313X-RAY DIFFRACTION85.86
2.56-2.650.30831340.22345306X-RAY DIFFRACTION86.96
2.65-2.760.2671370.21225361X-RAY DIFFRACTION87.49
2.76-2.880.261380.20515468X-RAY DIFFRACTION88.35
2.89-3.040.30741390.22015530X-RAY DIFFRACTION89.57
3.04-3.230.25281440.21045674X-RAY DIFFRACTION91.39
3.23-3.480.23141480.18295859X-RAY DIFFRACTION94.69
3.48-3.830.20411530.15956065X-RAY DIFFRACTION97.55
3.83-4.380.20461570.14146159X-RAY DIFFRACTION98.26
4.38-5.510.15481570.146260X-RAY DIFFRACTION99.03
5.52-47.30.22291660.17336587X-RAY DIFFRACTION99.34
Refinement TLS params.Method: refined / Origin x: -36.0351197821 Å / Origin y: -16.0723599577 Å / Origin z: 26.4064406277 Å
111213212223313233
T0.254631341776 Å2-0.00702974238449 Å20.0471828789836 Å2-0.323540563692 Å20.0113650339007 Å2--0.299191604915 Å2
L0.189316312471 °2-0.0450811842219 °2-0.0563272815576 °2-0.372709011918 °20.146707429555 °2--0.18062095907 °2
S0.0452899188309 Å °-0.0162306318544 Å °0.0662714224891 Å °-0.129918641826 Å °0.0318442505168 Å °-0.0238086530569 Å °-0.134126723395 Å °0.0108806450185 Å °-0.0781326523054 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