+Open data
-Basic information
Entry | Database: PDB / ID: 7x0d | ||||||
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Title | Crystal structure of phospholipase A1, CaPLA1 | ||||||
Components | Phospholipase A1 | ||||||
Keywords | HYDROLASE / Phospholipase A1 | ||||||
Function / homology | Phospholipase A1-II / phospholipase A1 activity / Fungal lipase-like domain / Lipase (class 3) / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / lipid catabolic process / Alpha/Beta hydrolase fold / Phospholipase A1 Function and homology information | ||||||
Biological species | Capsicum annuum (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3972515576 Å | ||||||
Authors | Heo, Y. / Lee, I. / Moon, S. / Lee, W. | ||||||
Funding support | 1items
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Citation | Journal: Molecules / Year: 2022 Title: Crystal Structures of the Plant Phospholipase A1 Proteins Reveal a Unique Dimerization Domain. Authors: Heo, Y. / Lee, I. / Moon, S. / Yun, J.H. / Kim, E.Y. / Park, S.Y. / Park, J.H. / Kim, W.T. / Lee, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x0d.cif.gz | 396.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x0d.ent.gz | 259.4 KB | Display | PDB format |
PDBx/mmJSON format | 7x0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x0d_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7x0d_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7x0d_validation.xml.gz | 56.7 KB | Display | |
Data in CIF | 7x0d_validation.cif.gz | 79.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/7x0d ftp://data.pdbj.org/pub/pdb/validation_reports/x0/7x0d | HTTPS FTP |
-Related structure data
Related structure data | 7x0cC 2yijS S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45267.461 Da / Num. of mol.: 4 / Mutation: Y113W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Capsicum annuum (plant) / Gene: PLA1, T459_03599 / Production host: Escherichia coli (E. coli) References: UniProt: A5YW95, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases #2: Chemical | ChemComp-SO4 / #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: 2.48 Å3/Da / Density % sol: 50.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES (pH 7.5), 0.2M ammonium sulfate, 10% PEG 8000, 10% 2-propanol |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.0082 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0082 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→50 Å / Num. obs: 67379 / % possible obs: 96.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 26.5624458342 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 13.97 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.79 / Num. unique obs: 3305 / % possible all: 95.5 |
-Processing
Software | Name: PHENIX / Version: 1.10.1_2155 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YIJ Resolution: 2.3972515576→49.1061888254 Å / SU ML: 0.336679155301 / Cross valid method: FREE R-VALUE / σ(F): 1.33340615603 / Phase error: 26.7039351573 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.5776849861 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3972515576→49.1061888254 Å
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Refine LS restraints |
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LS refinement shell |
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