+Open data
-Basic information
Entry | Database: PDB / ID: 1msi | ||||||
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Title | STRUCTURE OF ANTIFREEZE GLYCOPROTEIN QAE(HPLC 12) | ||||||
Components | TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 | ||||||
Keywords | ANTIFREEZE PROTEIN / MULTIGENE FAMILY / THERMAL HYSTERESIS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Macrozoarces americanus (ocean pout) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å | ||||||
Authors | Jia, Z. / Deluca, C.I. / Chao, H. / Davies, P.L. | ||||||
Citation | Journal: Nature / Year: 1996 Title: Structural basis for the binding of a globular antifreeze protein to ice. Authors: Jia, Z. / DeLuca, C.I. / Chao, H. / Davies, P.L. #1: Journal: Nature / Year: 1997 Title: Erratum. Structural Basis for the Binding of a Globular Antifreeze Protein to Ice Authors: Jia, Z. / Deluca, C.I. / Chao, H. / Davies, P.L. #2: Journal: Protein Sci. / Year: 1995 Title: Crystallization and Preliminary X-Ray Crystallographic Studies on Type III Antifreeze Protein Authors: Jia, Z. / Deluca, C.I. / Davies, P.L. #3: Journal: Protein Sci. / Year: 1993 Title: Use of Proline Mutants to Help Solve the NMR Solution Structure of Type III Antifreeze Protein Authors: Chao, H. / Davies, P.L. / Sykes, B.D. / Sonnichsen, F.D. #4: Journal: J.Biol.Chem. / Year: 1988 Title: Multiple Genes Provide the Basis for Antifreeze Protein Diversity and Dosage in the Ocean Pout, Macrozoarces Americanus Authors: Hew, C.L. / Wang, N.C. / Joshi, S. / Fletcher, G.L. / Scott, G.K. / Hayes, P.H. / Buettner, B. / Davies, P.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1msi.cif.gz | 30.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1msi.ent.gz | 21.1 KB | Display | PDB format |
PDBx/mmJSON format | 1msi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/1msi ftp://data.pdbj.org/pub/pdb/validation_reports/ms/1msi | HTTPS FTP |
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-Related 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: 7422.746 Da / Num. of mol.: 1 / Mutation: P64A, P65A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macrozoarces americanus (ocean pout) / Plasmid: PT7-7F / Production host: Escherichia coli (E. coli) / References: UniProt: P19614 |
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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: 1.92 Å3/Da / Density % sol: 30 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 4.5 / PH range high: 4 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.927 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 30, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.927 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. obs: 16529 / % possible obs: 96.6 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 15.46 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.25→1.31 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 1.64 / Rsym value: 0.557 / % possible all: 98.1 |
Reflection | *PLUS Num. measured all: 46873 |
Reflection shell | *PLUS % possible obs: 98.1 % |
-Processing
Software |
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Refinement | Resolution: 1.25→8 Å / Cross valid method: FREE R / σ(F): 0
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Displacement parameters | Biso mean: 18.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.31 Å
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.3109 |