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- PDB-6n5f: Crystal structure of an epoxide hydrolase from Trichoderma reesei... -

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Basic information

Entry
Database: PDB / ID: 6n5f
TitleCrystal structure of an epoxide hydrolase from Trichoderma reesei in complex with inhibitor 3
ComponentsEpoxide hydrolase TrEH
KeywordsHYDROLASE/INHIBITOR / Trichoderma reesei / epoxide hydrolase / inhibitor / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homologyepoxide hydrolase activity / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / N-(8-amino-8-oxooctyl)nonanamide / Predicted protein
Function and homology information
Biological speciesTrichoderma reesei QM9414 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsOliveira, 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)2015/03329-9 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 21, 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 TrEH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8332
Polymers37,5351
Non-polymers2981
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.005, 77.903, 88.196
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 TrEH


Mass: 37534.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma reesei QM9414 (fungus) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G0R7E2*PLUS
#2: Chemical ChemComp-KJ1 / N-(8-amino-8-oxooctyl)nonanamide


Mass: 298.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H34N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
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 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48 Å / Relative weight: 1
ReflectionResolution: 1.93→44.15 Å / Num. obs: 27141 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 26.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.152 / Net I/σ(I): 13.8 / Num. measured all: 349907
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.93-1.9812.21.6117830.792198.4
9.05-44.15100.0513170.998199.2

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Processing

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

5uro


Resolution: 1.93→44.15 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.6
RfactorNum. reflection% reflection
Rfree0.1985 1308 4.83 %
Rwork0.1662 --
obs0.1678 27089 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.14 Å2 / Biso mean: 28.5273 Å2 / Biso min: 16.55 Å2
Refinement stepCycle: final / Resolution: 1.93→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 21 223 2881
Biso mean--29.77 35.32 -
Num. residues----336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122738
X-RAY DIFFRACTIONf_angle_d1.0963712
X-RAY DIFFRACTIONf_chiral_restr0.063386
X-RAY DIFFRACTIONf_plane_restr0.007488
X-RAY DIFFRACTIONf_dihedral_angle_d17.8981634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9301-2.00740.24951510.2042785293699
2.0074-2.09870.19861310.186628302961100
2.0987-2.20940.20981410.173328352976100
2.2094-2.34780.2341440.166628122956100
2.3478-2.5290.23061520.167128432995100
2.529-2.78350.19991440.167628512995100
2.7835-3.18620.2051520.156828733025100
3.1862-4.01390.19011700.15228743044100
4.0139-44.16470.17091230.170130783201100

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