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Yorodumi- PDB-8qvm: Comparison of room-temperature and cryogenic structures of solubl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qvm | |||||||||||||||
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Title | Comparison of room-temperature and cryogenic structures of soluble Epoxide Hydrolase with ligands bound. | |||||||||||||||
Components | Bifunctional epoxide hydrolase 2 | |||||||||||||||
Keywords | HYDROLASE / Inhibitor / serial crystallography / drug discovery / fixed target / room temperature / microcrystals | |||||||||||||||
Function / homology | Function and homology information lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / phospholipid dephosphorylation / epoxide metabolic process / lipid phosphatase activity / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) ...lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / phospholipid dephosphorylation / epoxide metabolic process / lipid phosphatase activity / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / regulation of cholesterol metabolic process / dephosphorylation / phosphatase activity / peroxisomal matrix / toxic substance binding / cholesterol homeostasis / Peroxisomal protein import / response to toxic substance / peroxisome / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / extracellular exosome / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||||||||
Authors | Dunge, A. / Uwangue, O. / Phan, C. / Bjelcic, M. / Gunnarsson, J. / Wehlander, G. / Kack, H. / Branden, G. | |||||||||||||||
Funding support | Sweden, 4items
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Citation | Journal: Iucrj / Year: 2024 Title: Exploring serial crystallography for drug discovery. Authors: Dunge, A. / Phan, C. / Uwangue, O. / Bjelcic, M. / Gunnarsson, J. / Wehlander, G. / Kack, H. / Branden, G. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qvm.cif.gz | 125.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qvm.ent.gz | 95.7 KB | Display | PDB format |
PDBx/mmJSON format | 8qvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qvm_validation.pdf.gz | 439.4 KB | Display | wwPDB validaton report |
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Full document | 8qvm_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 8qvm_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 8qvm_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/8qvm ftp://data.pdbj.org/pub/pdb/validation_reports/qv/8qvm | HTTPS FTP |
-Related structure data
Related structure data | 8qvfC 8qvgC 8qvhC 8qvkC 8qvlC 8qwgC 8qwiC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 62002.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P34913 |
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#2: Chemical | ChemComp-PGE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.11 % / Description: Rods |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 8.2 Details: 32% PEG 3350, 0.1M Li2SO4 and 0.1M Tris-HCl (pH 8.2) |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.11 Å / Num. obs: 114534 / % possible obs: 100 % / Observed criterion σ(I): 0.7 / Redundancy: 66.33 % / Biso Wilson estimate: 42.73 Å2 / CC1/2: 0.9513 / R split: 0.1834 / Net I/σ(I): 3.66 |
Reflection shell | Resolution: 2→2.01 Å / Num. unique obs: 1938 / CC1/2: 0.45 / R split: 0.9691 |
Serial crystallography sample delivery | Description: silicon nitride membrane (Silson) / Method: fixed target |
Serial crystallography sample delivery fixed target | Description: silicon nitride membrane / Support base: cryo cap |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.11 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.17 / SU Rfree Blow DPI: 0.159 / SU Rfree Cruickshank DPI: 0.156
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Displacement parameters | Biso mean: 45.51 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→44.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.01 Å
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