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Yorodumi- PDB-6n5g: Crystal structure of an epoxide hydrolase from Trichoderma reesei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n5g | ||||||||||||||||||||||||||||||
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Title | Crystal structure of an epoxide hydrolase from Trichoderma reesei in complex with inhibitor 2 | ||||||||||||||||||||||||||||||
Components | Epoxide hydrolase TrEH | ||||||||||||||||||||||||||||||
Keywords | HYDROLASE/INHIBITOR / Trichoderma reesei / epoxide hydrolase / inhibitor / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information phospholipid dephosphorylation / lipid phosphatase activity / epoxide hydrolase activity / cholesterol homeostasis / peroxisome / magnesium ion binding Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Trichoderma reesei QM9414 (fungus) | ||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||||||||||||||||||||
Authors | 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, 9items
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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: de Oliveira, G.S. / Adriani, P.P. / Ribeiro, J.A. / Morisseau, C. / Hammock, B.D. / Dias, M.V.B. / 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 | 6n5g.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n5g.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 6n5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n5g_validation.pdf.gz | 663.2 KB | Display | wwPDB validaton report |
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Full document | 6n5g_full_validation.pdf.gz | 671.5 KB | Display | |
Data in XML | 6n5g_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 6n5g_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/6n5g ftp://data.pdbj.org/pub/pdb/validation_reports/n5/6n5g | HTTPS FTP |
-Related structure data
Related structure data | 6n3kC 6n3zC 6n5fC 6n5hC 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-KDS / |
#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: 2.25 Å3/Da / Density % sol: 45.37 % |
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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 PILATUS3 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: 2.6→38.66 Å / Num. obs: 10961 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 24.54 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.281 / Net I/σ(I): 7.5 / Num. measured all: 135942 / Scaling rejects: 58 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5uro Resolution: 2.6→37.814 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.04 Å2 / Biso mean: 24.9084 Å2 / Biso min: 7.89 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→37.814 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: 4
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