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- PDB-6n3k: Crystal structure of an epoxide hydrolase from Trichoderma reesei... -

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Basic information

Entry
Database: PDB / ID: 6n3k
TitleCrystal structure of an epoxide hydrolase from Trichoderma reesei in complex with inhibitor 1
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / Trichoderma reesei / epoxide hydrolase / inhibitor
Function / homologyepoxide hydrolase activity / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Chem-K9V / Predicted protein
Function and homology information
Biological speciesTrichoderma reesei QM9414 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
Authorsde Oliveira, G.S. / Adriani, P.P. / Ribeiro, J.A. / Morisseau, C. / Hammock, B.D. / Dias, M.V. / Chambergo, F.S.
Funding support Brazil, United States, 10items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/03329 Brazil
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)NIEHS-R01 ES002710 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)P42 ES 04699 United States
Sao Paulo Research Foundation (FAPESP)2014/24107-1 Brazil
Sao Paulo Research Foundation (FAPESP)2017/25705-8 Brazil
Sao Paulo Research Foundation (FAPESP)2015/09188-8 Brazil
Sao Paulo Research Foundation (FAPESP)2018/00351-1 Brazil
Sao Paulo Research Foundation (FAPESP)2016/12859-4 Brazil
Sao Paulo Research Foundation (FAPESP)2013/15906-5 Brazil
Fundacao para a Ciencia e a Tecnologia142311/2016-2 Brazil
CitationJournal: Int. J. Biol. Macromol. / Year: 2019
Title: The molecular structure of an epoxide hydrolase from Trichoderma reesei in complex with urea or amide-based inhibitors.
Authors: de Oliveira, G.S. / Adriani, P.P. / Ribeiro, J.A. / Morisseau, C. / Hammock, B.D. / Dias, M.V.B. / Chambergo, F.S.
History
DepositionNov 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9372
Polymers37,5351
Non-polymers4021
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.073, 77.276, 87.103
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 Epoxide hydrolase


Mass: 37534.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma reesei QM9414 (fungus) / Gene: TrEH
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G0R7E2*PLUS
#2: Chemical ChemComp-K9V / N-{cis-4-[(2,6-difluorophenyl)methoxy]cyclohexyl}-N'-(3-phenylpropyl)urea


Mass: 402.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28F2N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.52
Details: 50 mM 3-morpholinopropane-1-sulfonic acid (MOPS) pH 6.5, 40 mM potassium bromide and 44.6% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.48 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48 Å / Relative weight: 1
ReflectionResolution: 2.2→38.64 Å / Num. obs: 17796 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 25.04 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.19 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.2-2.27121.0415190.861100
9.07-38.647.70.0692980.998197.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.73 Å37.94 Å
Translation6.73 Å37.94 Å

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASER2.6.0phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5uro

5uro


Resolution: 2.2→37.941 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.15
RfactorNum. reflection% reflection
Rfree0.2483 868 4.91 %
Rwork0.1812 --
obs0.1843 17685 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.01 Å2 / Biso mean: 27.6705 Å2 / Biso min: 12.54 Å2
Refinement stepCycle: final / Resolution: 2.2→37.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 29 152 2818
Biso mean--39.05 32.53 -
Num. residues----336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072740
X-RAY DIFFRACTIONf_angle_d0.8823718
X-RAY DIFFRACTIONf_chiral_restr0.048387
X-RAY DIFFRACTIONf_plane_restr0.006487
X-RAY DIFFRACTIONf_dihedral_angle_d16.5991623
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.33780.24791330.191327602893100
2.3378-2.51830.29811480.19627612909100
2.5183-2.77160.25791760.191327522928100
2.7716-3.17250.26491260.18328152941100
3.1725-3.99640.21791240.16562825294999
3.9964-37.94650.2431610.18122904306598

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