[English] 日本語
Yorodumi
- PDB-5yqt: Crystal Structure of the L74F/M78V/I80V/L114F mutant of LEH compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yqt
TitleCrystal Structure of the L74F/M78V/I80V/L114F mutant of LEH complexed with cyclopentene oxide
ComponentsLimonene-1,2-epoxide hydrolase
KeywordsHYDROLASE / epoxide hydrolase
Function / homology
Function and homology information


limonene-1,2-epoxide hydrolase / limonene-1,2-epoxide hydrolase activity
Similarity search - Function
Limonene-1,2-epoxide hydrolase / Limonene-1,2-epoxide hydrolase catalytic domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
(1R,5S)-6-oxabicyclo[3.1.0]hexane / Limonene-1,2-epoxide hydrolase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Model detailsA mutant of limonene 1,2-epoxide hydrolase
AuthorsKong, X.D. / Sun, Z.T. / Wu, L. / Reetz, M.T. / Zhou, J.H. / Xu, J.H.
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Structural and Computational Insight into the Catalytic Mechanism of Limonene Epoxide Hydrolase Mutants in Stereoselective Transformations.
Authors: Sun, Z. / Wu, L. / Bocola, M. / Chan, H.C.S. / Lonsdale, R. / Kong, X.D. / Yuan, S. / Zhou, J. / Reetz, M.T.
History
DepositionNov 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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
C: Limonene-1,2-epoxide hydrolase
D: Limonene-1,2-epoxide hydrolase
A: Limonene-1,2-epoxide hydrolase
B: Limonene-1,2-epoxide hydrolase
E: Limonene-1,2-epoxide hydrolase
F: Limonene-1,2-epoxide hydrolase
G: Limonene-1,2-epoxide hydrolase
H: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,37613
Polymers138,9558
Non-polymers4215
Water7,386410
1
C: Limonene-1,2-epoxide hydrolase
D: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9074
Polymers34,7392
Non-polymers1682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-12 kcal/mol
Surface area12400 Å2
MethodPISA
2
A: Limonene-1,2-epoxide hydrolase
B: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9074
Polymers34,7392
Non-polymers1682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-11 kcal/mol
Surface area12250 Å2
MethodPISA
3
E: Limonene-1,2-epoxide hydrolase
F: Limonene-1,2-epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)34,7392
Polymers34,7392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-14 kcal/mol
Surface area12530 Å2
MethodPISA
4
G: Limonene-1,2-epoxide hydrolase
H: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8233
Polymers34,7392
Non-polymers841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-14 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.254, 60.677, 118.759
Angle α, β, γ (deg.)90.00, 90.53, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Limonene-1,2-epoxide hydrolase


Mass: 17369.381 Da / Num. of mol.: 8 / Mutation: L74F, M78V, I80V, L114F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: limA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase
#2: Chemical
ChemComp-3ZS / (1R,5S)-6-oxabicyclo[3.1.0]hexane


Mass: 84.116 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.4 M citrate sodium

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 24, 2014
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 63084 / % possible obs: 95 % / Redundancy: 4.4 % / Net I/σ(I): 7.787
Reflection shellResolution: 2.3→2.38 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XBY

4xby


Resolution: 2.3→30.155 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2833 3117 4.94 %
Rwork0.2241 --
obs0.227 63039 94.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→30.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8936 0 30 410 9376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099244
X-RAY DIFFRACTIONf_angle_d0.92312585
X-RAY DIFFRACTIONf_dihedral_angle_d15.2935472
X-RAY DIFFRACTIONf_chiral_restr0.0531399
X-RAY DIFFRACTIONf_plane_restr0.0071639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.33610.35421560.29312745X-RAY DIFFRACTION96
2.3361-2.37430.3181500.26282791X-RAY DIFFRACTION99
2.3743-2.41530.35351730.2552832X-RAY DIFFRACTION99
2.4153-2.45920.35711320.26052800X-RAY DIFFRACTION99
2.4592-2.50640.30331350.26352811X-RAY DIFFRACTION98
2.5064-2.55760.37661370.25462812X-RAY DIFFRACTION98
2.5576-2.61320.28771440.25362808X-RAY DIFFRACTION98
2.6132-2.67390.31421450.24432779X-RAY DIFFRACTION98
2.6739-2.74070.29871650.23292767X-RAY DIFFRACTION98
2.7407-2.81480.31871490.22912773X-RAY DIFFRACTION98
2.8148-2.89750.27251510.23052797X-RAY DIFFRACTION97
2.8975-2.9910.28491410.22632740X-RAY DIFFRACTION97
2.991-3.09780.2891670.22322744X-RAY DIFFRACTION96
3.0978-3.22170.27261520.2312770X-RAY DIFFRACTION96
3.2217-3.36810.31251540.22732737X-RAY DIFFRACTION96
3.3681-3.54540.28821380.22352682X-RAY DIFFRACTION93
3.5454-3.76720.29821110.21442607X-RAY DIFFRACTION90
3.7672-4.05740.27211250.21332640X-RAY DIFFRACTION92
4.0574-4.46460.2531270.19772461X-RAY DIFFRACTION85
4.4646-5.10790.22191250.19162362X-RAY DIFFRACTION82
5.1079-6.42510.24221210.2122753X-RAY DIFFRACTION94
6.4251-30.15730.26791190.22132711X-RAY DIFFRACTION89

+
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