+Open data
-Basic information
Entry | Database: PDB / ID: 4msi | ||||||
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Title | TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 | ||||||
Components | TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 | ||||||
Keywords | ANTIFREEZE / ANTIFREEZE POLYPEPTIDE / MUTANT / ICE BINDING PROTEIN / THERMAL HYSTERESIS PROTEIN / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Macrozoarces americanus (ocean pout) | ||||||
Method | X-RAY DIFFRACTION / ISOMORPHOUS / Resolution: 1.6 Å | ||||||
Authors | Deluca, C.I. / Davies, P.L. / Ye, Q. / Jia, Z. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: The effects of steric mutations on the structure of type III antifreeze protein and its interaction with ice. Authors: DeLuca, C.I. / Davies, P.L. / Ye, Q. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4msi.cif.gz | 20.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4msi.ent.gz | 15.1 KB | Display | PDB format |
PDBx/mmJSON format | 4msi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/4msi ftp://data.pdbj.org/pub/pdb/validation_reports/ms/4msi | HTTPS FTP |
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-Related structure data
Related structure data | 2msiC 3msiC 5msiC 6msiC 7msiC 1msiS S: Starting model for refinement C: citing same article (ref.) |
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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: 7026.352 Da / Num. of mol.: 1 / Mutation: A16T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macrozoarces americanus (ocean pout) / Plasmid: PT7-7F-PGP1-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM 83 / 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: 2.1 Å3/Da / Density % sol: 30 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 Details: PROTEIN WAS CRYSTALLIZED IN 50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5 PH range: 4-4.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Jia, Z.,(1995) Protein Sci., 4, 1236. / PH range low: 4.5 / PH range high: 4 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 11, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 8057 / % possible obs: 95.2 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.059 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.6→1.67 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.267 / % possible all: 88.9 |
Reflection | *PLUS Num. measured all: 28480 / Rmerge(I) obs: 0.059 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS Starting model: 1MSI Resolution: 1.6→50 Å / Cross valid method: FREE-R REFINEMENT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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LS refinement shell | Resolution: 1.6→1.67 Å / Total num. of bins used: 8 / % reflection obs: 93.94 % | ||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Num. reflection obs: 8075 / Rfactor Rwork: 0.26 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |