[English] 日本語
Yorodumi
- PDB-3g02: Structure of enantioselective mutant of epoxide hydrolase from As... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3g02
TitleStructure of enantioselective mutant of epoxide hydrolase from Aspergillus niger generated by directed evolution
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / EPOXIDE HYDROLASE / ALPHA/BETA HYDROLASE FOLD / enantioselective / mutant / directed evolution
Function / homology
Function and homology information


epoxide hydrolase / epoxide metabolic process / epoxide hydrolase activity
Similarity search - Function
Epoxide hydrolase, N-terminal / Epoxide hydrolase N terminus / Epoxide hydrolase / Epoxide hydrolase-like / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Epoxide hydrolase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsNaworyta, A. / Mowbray, S.L.
Citation
Journal: J.Am.Chem.Soc. / Year: 2009
Title: Directed evolution of an enantioselective epoxide hydrolase: uncovering the source of enantioselectivity at each evolutionary stage
Authors: Reetz, M.T. / Bocola, M. / Wang, L.-W. / Sanchis, J. / Cronin, A. / Arand, M. / Zou, J. / Archelas, A. / Bottalla, A.-L. / Naworyta, A. / Mowbray, S.L.
#1: Journal: Structure / Year: 2000
Title: Structure of Aspergillus niger epoxide hydrolase at 1.8 A resolution: implications for the structure and function of the mammalian microsomal class of epoxide hydrolases
Authors: Zou, J. / Hallberg, B.M. / Bergfors, T. / Oesch, F. / Arand, M. / Mowbray, S.L. / Jones, T.A.
History
DepositionJan 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Epoxide hydrolase
B: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2325
Polymers92,0942
Non-polymers1383
Water12,719706
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-24 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.866, 89.675, 75.344
Angle α, β, γ (deg.)90.000, 104.790, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Epoxide hydrolase


Mass: 46047.125 Da / Num. of mol.: 2 / Fragment: residues 5-398
Mutation: L215F, A217N, R219S, L249Y, T317W, T318V, M329P, L330Y, C350V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Strain: LCP521 / Gene: hyl1 / Plasmid: pQEEH_LW202 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q9UR30, microsomal epoxide hydrolase
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 706 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG 6000, 0.1M MES, pH 6.0, 0.1M unbuffered sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 31, 2007
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.5→30.54 Å / Num. all: 209428 / Num. obs: 120696 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 15.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 7.2 / Num. unique all: 18142 / % possible all: 98.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.91 Å
Translation2.5 Å28.91 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QO7

1qo7


Resolution: 1.5→28.91 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.877 / SU B: 1.201 / SU ML: 0.046 / SU R Cruickshank DPI: 0.082 / SU Rfree: 0.079 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 6102 5.1 %RANDOM
Rwork0.183 ---
all0.184 126958 --
obs0.184 120661 95.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.51 Å2 / Biso mean: 15.23 Å2 / Biso min: 3.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-0.64 Å2
2--0.95 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6354 0 0 715 7069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226587
X-RAY DIFFRACTIONr_angle_refined_deg1.0071.9599001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4165815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02723.31290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.041151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7911535
X-RAY DIFFRACTIONr_chiral_restr0.0690.2957
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025155
X-RAY DIFFRACTIONr_nbd_refined0.1860.23503
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24630
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2597
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.258
X-RAY DIFFRACTIONr_mcbond_it0.4481.54106
X-RAY DIFFRACTIONr_mcangle_it0.75926542
X-RAY DIFFRACTIONr_scbond_it1.14332846
X-RAY DIFFRACTIONr_scangle_it1.754.52459
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 435 -
Rwork0.225 8756 -
all-9191 -
obs--98.12 %

+
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