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Yorodumi- PDB-3gbo: Crystal structure of BmooMPalpha-I, a non-hemorrhagic metalloprot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gbo | ||||||
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Title | Crystal structure of BmooMPalpha-I, a non-hemorrhagic metalloproteinase isolated from Bothrops moojeni snake venom | ||||||
Components | Zinc metalloproteinase BmooMPalfa-I | ||||||
Keywords | HYDROLASE / snake venom metalloproteinase / Metal-binding / Metalloprotease / Protease / Secreted / Toxin / Zinc | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bothrops moojeni (Brazilian lancehead) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Akao, P.K. / Tonoli, C.C.C. / Murakami, M.T. | ||||||
Citation | Journal: Toxicon / Year: 2010 Title: Structural studies of BmooMPalpha-I, a non-hemorrhagic metalloproteinase from Bothrops moojeni venom. Authors: Akao, P.K. / Tonoli, C.C. / Navarro, M.S. / Cintra, A.C. / Neto, J.R. / Arni, R.K. / Murakami, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gbo.cif.gz | 52 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gbo.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 3gbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/3gbo ftp://data.pdbj.org/pub/pdb/validation_reports/gb/3gbo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22698.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bothrops moojeni (Brazilian lancehead) / Tissue: Venom References: UniProt: P85314, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: PEG 8000, Tris buffer, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.428 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 10, 2009 |
Radiation | Monochromator: Sagital Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.428 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→20.8 Å / Num. all: 19460 / Num. obs: 19308 / % possible obs: 94.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.76→1.83 Å / % possible all: 66.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→20.8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.508 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.122 / ESU R Free: 0.123 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.737 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→20.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.81 Å / Total num. of bins used: 20
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