[English] 日本語
Yorodumi
- PDB-3g0i: Complex of Aspergillus niger epoxide hydrolase with valpromide (2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3g0i
TitleComplex of Aspergillus niger epoxide hydrolase with valpromide (2-propylpentanamide)
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / Epoxide hydrolase / alpha/beta hydrolase fold / valpromide / 2-propylpentanamide
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
2-PROPYLPENTANAMIDE / Epoxide hydrolase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZou, J. / 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 28, 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 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
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)88,5354
Polymers88,2482
Non-polymers2862
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-16 kcal/mol
Surface area28310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.985, 89.655, 75.812
Angle α, β, γ (deg.)90.000, 105.310, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Epoxide hydrolase


Mass: 44124.180 Da / Num. of mol.: 2 / Fragment: UNP residues 5-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Strain: LCP521 / Gene: hyl1 / Plasmid: PGEF-ANEH336 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UR30, microsomal epoxide hydrolase
#2: Chemical ChemComp-VPR / 2-PROPYLPENTANAMIDE / VALPROMIDE


Mass: 143.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG6000, 0.1M MES, pH6.0, 0.1M unbuffered sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 1999
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 47596 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066 / Χ2: 0.877 / Net I/σ(I): 16.947
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.213 / Num. unique all: 2189 / Χ2: 0.993 / % possible all: 92.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QO7

1qo7


Resolution: 2.1→38.21 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.231 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1214 2.6 %RANDOM
Rwork0.175 ---
all0.176 47498 --
obs0.176 47296 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.58 Å2 / Biso mean: 14.057 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.03 Å2
2--0.1 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6218 0 20 454 6692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226439
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.9678771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41923.214280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.657151031
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3751537
X-RAY DIFFRACTIONr_chiral_restr0.080.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024979
X-RAY DIFFRACTIONr_nbd_refined0.1870.23144
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2517
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.212
X-RAY DIFFRACTIONr_mcbond_it0.5631.54041
X-RAY DIFFRACTIONr_mcangle_it0.93126379
X-RAY DIFFRACTIONr_scbond_it1.44132767
X-RAY DIFFRACTIONr_scangle_it2.2834.52392
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 78 -
Rwork0.182 3226 -
all-3304 -
obs--94.94 %

+
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