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Yorodumi- PDB-2zib: Crystal structure analysis of calcium-independent type II antifre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zib | ||||||
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Title | Crystal structure analysis of calcium-independent type II antifreeze protein | ||||||
Components | Type II antifreeze protein | ||||||
Keywords | ANTIFREEZE PROTEIN / THERMAL HYSTERESIS / Lectin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Brachyopsis rostratus (fish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.34 Å | ||||||
Authors | Nishimiya, Y. / Sato, R. / Kondo, H. / Noro, N. / Sugimoto, H. / Suzuki, M. / Tsuda, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal structure and mutational analysis of Ca2+-independent type II antifreeze protein from longsnout poacher, Brachyopsis rostratus Authors: Nishimiya, Y. / Kondo, H. / Takamichi, M. / Sugimoto, H. / Suzuki, M. / Miura, A. / Tsuda, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zib.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zib.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zib_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
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Full document | 2zib_full_validation.pdf.gz | 428.4 KB | Display | |
Data in XML | 2zib_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 2zib_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/2zib ftp://data.pdbj.org/pub/pdb/validation_reports/zi/2zib | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14518.515 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brachyopsis rostratus (fish) / Plasmid: PPICZALPHAA / Production host: PICHIA PASTORIS (fungus) / References: UniProt: A0ZT93 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.15 Å3/Da / Density % sol: 42.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.1M MES, 2M AMMONIUM SULFATE, pH 5.40, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→20 Å / Num. obs: 28592 / Biso Wilson estimate: 9.82 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.34→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.627 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.049 / 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: 14.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.34→1.38 Å / Total num. of bins used: 20
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