+Open data
-Basic information
Entry | Database: PDB / ID: 8jy1 | ||||||
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Title | Structure of Mangifera Indica Epoxide hydrolase 2 | ||||||
Components | Epoxide hydrolase-2 | ||||||
Keywords | PLANT PROTEIN / alpha-beta hydrolase epoxide hydrolase | ||||||
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 | Mangifera indica (mango) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Bhoite, A.S. / Gupta, V.S. / Kulkarni, K.A. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Structure of Mangifera Indica Epoxide hydrolase 2 Authors: Bhoite, A.S. / Gupta, V.S. / Kulkarni, K.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jy1.cif.gz | 241.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jy1.ent.gz | 194 KB | Display | PDB format |
PDBx/mmJSON format | 8jy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jy1_validation.pdf.gz | 685.8 KB | Display | wwPDB validaton report |
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Full document | 8jy1_full_validation.pdf.gz | 688.1 KB | Display | |
Data in XML | 8jy1_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 8jy1_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/8jy1 ftp://data.pdbj.org/pub/pdb/validation_reports/jy/8jy1 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36703.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mangifera indica (mango) / Gene: EH2 / Plasmid: pEXP5-CT/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): RIL / References: UniProt: A0A1U9ZCB5 #2: Chemical | ChemComp-PG4 / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M trisodium citrate, 0.2M ammonium acetate, 30%w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.6 Å / Num. obs: 34442 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.029 / Rrim(I) all: 0.104 / Net I/σ(I): 21.3 / Num. measured all: 447486 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.907 / Num. measured all: 46837 / Num. unique obs: 3542 / CC1/2: 0.891 / Rpim(I) all: 0.258 / Rrim(I) all: 0.943 / Net I/σ(I) obs: 2.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.6 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→47.6 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.86 Å / Origin y: 40.1446 Å / Origin z: 59.7091 Å
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Refinement TLS group | Selection details: all |