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Yorodumi- PDB-3hzd: Crystal structure of bothropstoxin-I (BthTX-I), a PLA2 homologue ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hzd | ||||||
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Title | Crystal structure of bothropstoxin-I (BthTX-I), a PLA2 homologue from Bothrops jararacussu venom | ||||||
Components | Phospholipase A2 homolog bothropstoxin-1 | ||||||
Keywords | TOXIN / Bothrops / snake venom / Phospholipase A2 / Lys49-PLA2s / myotoxicity / Antibiotic / Antimicrobial / Disulfide bond / Myotoxin / Secreted | ||||||
Function / homology | Function and homology information calcium-dependent phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / heparin binding / toxin activity / defense response to bacterium / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Bothrops jararacussu (jararacussu) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Silva, M.C.O. / Marchi-Salvador, D.P. / Fernandes, C.A.H. / Soares, A.M. / Fontes, M.R.M. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2010 Title: Comparison between apo and complexed structures of bothropstoxin-I reveals the role of Lys122 and Ca(2+)-binding loop region for the catalytically inactive Lys49-PLA(2)s. Authors: Fernandes, C.A. / Marchi-Salvador, D.P. / Salvador, G.M. / Silva, M.C. / Costa, T.R. / Soares, A.M. / Fontes, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hzd.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hzd.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/3hzd ftp://data.pdbj.org/pub/pdb/validation_reports/hz/3hzd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13753.136 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: The bothropstoxin-I was isolated from the Bothrops jararacussu venom. Source: (natural) Bothrops jararacussu (jararacussu) / Tissue: venom / References: UniProt: Q90249 #2: Chemical | ChemComp-LI / | #3: Water | ChemComp-HOH / | |
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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: 2.08 Å3/Da / Density % sol: 40.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 26% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.425 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 14, 2007 |
Radiation | Monochromator: Si curved crystal asymmetrically-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.425 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→26.64 Å / Num. all: 17151 / Num. obs: 16208 / % possible obs: 92 % / Observed criterion σ(I): 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model not deposited in the PDB but described in paper by M.T. da Silva-Giotto et al., Proteins (1998), 30, pp. 442 454. Resolution: 1.91→26.64 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / SU B: 11.725 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.503 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→26.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.96 Å / Total num. of bins used: 20
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