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- PDB-5uro: Structure of a soluble epoxide hydrolase identified in Trichoderm... -

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Basic information

Entry
Database: PDB / ID: 5uro
TitleStructure of a soluble epoxide hydrolase identified in Trichoderma reesei
ComponentsPredicted protein
KeywordsHYDROLASE / epoxide hydrolase / Trichoderma reesei
Function / homology
Function and homology information


phospholipid dephosphorylation / lipid phosphatase activity / epoxide hydrolase activity / cholesterol homeostasis / peroxisome / magnesium ion binding
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
2,2'-oxydi(ethyn-1-ol) / Predicted protein
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.701 Å
AuthorsWilson, C. / de Oliveira, G. / Chambergo, F. / Dias, M.V.B.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP) Brazil
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Structure of a soluble epoxide hydrolase identified in Trichoderma reesei.
Authors: Wilson, C. / De Oliveira, G.S. / Adriani, P.P. / Chambergo, F.S. / Dias, M.V.B.
History
DepositionFeb 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6332
Polymers37,5351
Non-polymers981
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.427, 78.281, 87.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Predicted protein


Mass: 37534.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (strain QM6a) (fungus)
Strain: QM6a / Gene: TRIREDRAFT_53220 / Production host: Escherichia coli 55989 (bacteria) / References: UniProt: G0R7E2
#2: Chemical ChemComp-8LD / 2,2'-oxydi(ethyn-1-ol)


Mass: 98.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.701→44.32 Å / Num. obs: 74551 / % possible obs: 99 % / Redundancy: 12.9 % / Net I/σ(I): 1.34

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.72 Å44.32 Å
Translation6.72 Å44.32 Å

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIX1.8.4_1496refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ans

3ans


Resolution: 1.701→44.32 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.62
RfactorNum. reflection% reflection
Rfree0.2106 3768 5.05 %
Rwork0.1827 --
obs0.1841 74551 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.05 Å2 / Biso mean: 41.9977 Å2 / Biso min: 24.88 Å2
Refinement stepCycle: final / Resolution: 1.701→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 7 179 2823
Biso mean--49.1 44.09 -
Num. residues----336

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