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Yorodumi- PDB-6al3: Lys49 PLA2 BPII derived from the venom of Protobothrops flavoviridis. -
+Open data
-Basic information
Entry | Database: PDB / ID: 6al3 | ||||||
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Title | Lys49 PLA2 BPII derived from the venom of Protobothrops flavoviridis. | ||||||
Components | Basic phospholipase A2 BP-II | ||||||
Keywords | TOXIN / Phospholipase A2 / toxic components / nake venom | ||||||
Function / homology | Function and homology information phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Protobothrops flavoviridis (habu) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.57 Å | ||||||
Authors | Matsui, T. / Kamata, S. / Suzuki, A. / Oda-Ueda, N. / Ogawa, T. / Tanaka, Y. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: SDS-induced oligomerization of Lys49-phospholipase A2from snake venom. Authors: Matsui, T. / Kamata, S. / Ishii, K. / Maruno, T. / Ghanem, N. / Uchiyama, S. / Kato, K. / Suzuki, A. / Oda-Ueda, N. / Ogawa, T. / Tanaka, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6al3.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6al3.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 6al3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6al3_validation.pdf.gz | 471.5 KB | Display | wwPDB validaton report |
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Full document | 6al3_full_validation.pdf.gz | 487.4 KB | Display | |
Data in XML | 6al3_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 6al3_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/6al3 ftp://data.pdbj.org/pub/pdb/validation_reports/al/6al3 | HTTPS FTP |
-Related structure data
Related structure data | 5vfhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: CYS / End label comp-ID: CYS / Auth seq-ID: 1 - 122 / Label seq-ID: 1 - 122
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-Components
#1: Protein | Mass: 13789.205 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Protobothrops flavoviridis (habu) / References: UniProt: P0DJJ9, phospholipase A2 #2: Chemical | |
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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: 2.73 Å3/Da / Density % sol: 55.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 100 mM Sodium acetate pH 4.2, 0.5 M Ammonium acetate, 32.5% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 11, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.49 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.57→45.363 Å / Num. obs: 19245 / % possible obs: 99.9 % / Redundancy: 6.736 % / CC1/2: 1 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.134 / Χ2: 1.156 / Net I/σ(I): 12.62 / Num. measured all: 129632 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.517
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VFH Resolution: 2.57→45.363 Å / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 24.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 117.14 Å2 / Biso mean: 42.9785 Å2 / Biso min: 30.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.57→45.363 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 95 %
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