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- PDB-3hzw: Crystal structure of bothropstoxin-I chemically modified by p-bro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hzw | |||||||||
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Title | Crystal structure of bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB) | |||||||||
![]() | Phospholipase A2 homolog bothropstoxin-1 | |||||||||
![]() | TOXIN / Lys49-PLA2 / Phospholipase homologue / myotoxicity / p-bromophenacyl bromide / Bothropstoxin-I / Antibiotic / Antimicrobial / Disulfide bond / Myotoxin / Secreted | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fernandes, C.A.H. / Marchi-Salvador, D.P. / Soares, A.M. / Fontes, M.R.M. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.4 KB | Display | ![]() |
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PDB format | ![]() | 48.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 837.2 KB | Display | ![]() |
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Full document | ![]() | 851.6 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hzdSC ![]() 3i03C ![]() 3i3iC ![]() 3iq3C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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 Bothrops jararacussu venom. Source: (natural) ![]() #2: Chemical | #3: Chemical | ChemComp-IPA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% w/v PEG 4000, 20% w/v Isopropanol, 0.1 M Sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 14, 2006 |
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: 2.28→50.77 Å / Num. all: 12419 / Num. obs: 11778 / % possible obs: 94.8 % / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.28→2.36 Å / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3HZD Resolution: 2.28→50.77 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.922 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.249 / 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: 48.739 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→50.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.339 Å / Total num. of bins used: 20
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