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Yorodumi- PDB-3iq3: Crystal Structure of Bothropstoxin-I complexed with polietilene g... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iq3 | ||||||
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Title | Crystal Structure of Bothropstoxin-I complexed with polietilene glicol 4000 - crystallized at 283 K | ||||||
Components | Phospholipase A2 homolog bothropstoxin-1 | ||||||
Keywords | TOXIN / Homologue Phospholipase A2 / Bothropstoxin-I / BthTX-I_10C / Lys49-PLA2 from Bothrops jararacussu / Snake venom / 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: 1.55 Å | ||||||
Authors | Salvador, G.H.M. / Marchi-Salvador, D.P. / Silva, M.C.O. / 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. #1: Journal: To be Published Title: Structure of Bothropstoxin-I Chemically Modified by p-Bromophenacyl Bromide Reveals Importante Structural Changes Associated With the Inhibition of Myotoxic Activity Authors: Salvador, G.H.M. / Marchi-Salvador, D.P. / Silva, M.C.O. / Soares, A.M. / Fontes, M.R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iq3.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iq3.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 3iq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/3iq3 ftp://data.pdbj.org/pub/pdb/validation_reports/iq/3iq3 | HTTPS FTP |
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-Related structure data
Related structure data | 3hzdSC 3hzwC 3i03C 3i3iC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13752.150 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Venom Glands / Source: (natural) Bothrops jararacussu (jararacussu) / References: UniProt: Q90249 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | D TO N CONFLICT IN UNP ENTRY Q90249 | |
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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: 2.12 Å3/Da / Density % sol: 41.9 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 29% PEG 4000, 0.1M Tris HCl, 0.2M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283.0K |
-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: Oct 10, 2007 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL - 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: 1.55→50 Å / Num. obs: 32689 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 12.73 |
Reflection shell | Resolution: 1.55→1.62 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.82 / Rsym value: 0.439 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry (3HZD) Resolution: 1.55→18.32 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.573 / SU ML: 0.074 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.105 / 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: 30.019 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→18.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.592 Å / Total num. of bins used: 20
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