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Yorodumi- PDB-3vn3: Fungal antifreeze protein exerts hyperactivity by constructing an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vn3 | ||||||
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Title | Fungal antifreeze protein exerts hyperactivity by constructing an inequable beta-helix | ||||||
Components | Antifreeze protein | ||||||
Keywords | ANTIFREEZE PROTEIN / right-handed beta-helix | ||||||
Function / homology | Ice-binding protein / Ice-binding-like / Ice-binding protein K3-B1 Function and homology information | ||||||
Biological species | Typhula ishikariensis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.95 Å | ||||||
Authors | Kondo, H. / Xiao, N. / Hanada, Y. / Sugimoto, H. / Hoshino, T. / Garnham, C.P. / Davies, P.L. / Tsuda, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Ice-binding site of snow mold fungus antifreeze protein deviates from structural regularity and high conservation Authors: Kondo, H. / Hanada, Y. / Sugimoto, H. / Hoshino, T. / Garnham, C.P. / Davies, P.L. / Tsuda, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vn3.cif.gz | 196.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vn3.ent.gz | 164.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vn3_validation.pdf.gz | 447.9 KB | Display | wwPDB validaton report |
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Full document | 3vn3_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 3vn3_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 3vn3_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/3vn3 ftp://data.pdbj.org/pub/pdb/validation_reports/vn/3vn3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22307.771 Da / Num. of mol.: 2 / Fragment: UNP residues 21-243 / Source method: isolated from a natural source / Source: (natural) Typhula ishikariensis (fungus) / Strain: BRB-1 / References: UniProt: Q76CE6 #2: Chemical | ChemComp-EDO / #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: 2.23 Å3/Da / Density % sol: 44.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: 0.1M Bis-Tris, 1.0M ammonium sulfate, 0.1M sodium chloride, pH 6.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 18, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→34.41 Å / Num. obs: 232289 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 0.95→1 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2 / Num. unique all: 32714 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 0.95→34.41 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.373 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.482 Å2
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Refinement step | Cycle: LAST / Resolution: 0.95→34.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.95→0.975 Å / Total num. of bins used: 20
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