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Yorodumi- PDB-1ops: ICE-BINDING SURFACE ON A TYPE III ANTIFREEZE PROTEIN FROM OCEAN POUT -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ops | ||||||
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Title | ICE-BINDING SURFACE ON A TYPE III ANTIFREEZE PROTEIN FROM OCEAN POUT | ||||||
Components | TYPE III ANTIFREEZE PROTEIN | ||||||
Keywords | ANTIFREEZE PROTEIN / ICE CRYSTAL GROWTH INHIBITION / PRETZEL FOLD / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Macrozoarces americanus (ocean pout) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Yang, D.S.C. / Hon, W.-C. / Bubanko, S. / Xue, Y. / Seetharaman, J. / Hew, C.L. / Sicheri, F. | ||||||
Citation | Journal: Biophys.J. / Year: 1998 Title: Identification of the ice-binding surface on a type III antifreeze protein with a "flatness function" algorithm. Authors: Yang, D.S. / Hon, W.C. / Bubanko, S. / Xue, Y. / Seetharaman, J. / Hew, C.L. / Sicheri, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ops.cif.gz | 22.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ops.ent.gz | 13.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ops.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ops_validation.pdf.gz | 420.5 KB | Display | wwPDB validaton report |
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Full document | 1ops_full_validation.pdf.gz | 421.4 KB | Display | |
Data in XML | 1ops_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 1ops_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/1ops ftp://data.pdbj.org/pub/pdb/validation_reports/op/1ops | 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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Unit cell |
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-Components
#1: Protein | Mass: 6750.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOFORM HPLC-3 / Source: (natural) Macrozoarces americanus (ocean pout) / Tissue: SERUM / References: UniProt: P19608 |
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#2: 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: 2.05 Å3/Da / Density % sol: 40.05 % Description: THE STRUCTURE WAS SOLVED BY THE METHOD OF ITERATIVE SINGLE ANOMALOUS SCATTERING (B.C. WANG, (1985), METHODS ENZYMOL., 114, P90-117). | ||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1993 / Details: SUPPER DOUBLE FOCUSING MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 3107 / % possible obs: 82.4 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.066 |
Reflection | *PLUS Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 54.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: THE STARTING STRUCTURAL MODEL WAS DETERMINED FROM A CRYSTAL GROWN WITH THE RECOMBINANT, SINGLY-IODINATED PROTEIN, ISOFORM HPLC-6. THIS MODEL IS NOT YET AVAILABLE. Resolution: 2→40 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK ENT MODEL USED
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Displacement parameters | Biso mean: 17.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 40 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.318 |