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Yorodumi- PDB-6n5h: Crystal structure of an epoxide hydrolase from Trichoderma reesei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n5h | |||||||||||||||||||||||||||||||||
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Title | Crystal structure of an epoxide hydrolase from Trichoderma reesei in complex with inhibitor 5 | |||||||||||||||||||||||||||||||||
Components | Epoxide hydrolase TrEH | |||||||||||||||||||||||||||||||||
Keywords | HYDROLASE/INHIBITOR / Trichoderma reesei / epoxide hydrolase / inhibitor / HYDROLASE / HYDROLASE-INHIBITOR complex | |||||||||||||||||||||||||||||||||
Function / homology | epoxide hydrolase activity / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Chem-AUB / Predicted protein Function and homology information | |||||||||||||||||||||||||||||||||
Biological species | Trichoderma reesei QM9414 (fungus) | |||||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.717 Å | |||||||||||||||||||||||||||||||||
Authors | Oliveira, G.S. / Adriano, P.P. / Ribeiro, J.A. / Morisseau, C. / Hammock, B.D. / Dias, M.V. / Chambergo, F.S. | |||||||||||||||||||||||||||||||||
Funding support | Brazil, United States, 10items
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Citation | Journal: 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: Oliveira, G.S. / Adriano, P.P. / Ribeiro, J.A. / Morisseau, C. / Hammock, B.D. / Dias, M.V. / Chambergo, F.S. | |||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n5h.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n5h.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 6n5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/6n5h ftp://data.pdbj.org/pub/pdb/validation_reports/n5/6n5h | HTTPS FTP |
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-Related structure data
Related structure data | 6n3kC 6n3zC 6n5fC 6n5gC 5uroS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-AUB / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.98 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.48 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 10, 2017 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.48 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.72→42.23 Å / Num. obs: 36609 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.7 / Num. measured all: 227659 / Scaling rejects: 8 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5uro Resolution: 1.717→35.469 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.25 Å2 / Biso mean: 24.2134 Å2 / Biso min: 11.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.717→35.469 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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