+Open data
-Basic information
Entry | Database: PDB / ID: 2spg | ||||||
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Title | TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T15S | ||||||
Components | PROTEIN (ANTIFREEZE PROTEIN TYPE III) | ||||||
Keywords | ANTIFREEZE PROTEIN / MUTANT / ICE BINDING PROTEIN / THERMAL HYSTERESIS PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Macrozoarces americanus (ocean pout) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.75 Å | ||||||
Authors | Graether, S.P. / Deluca, C.I. / Baardsnes, J. / Hill, G.A. / Davies, P.L. / Jia, Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: Quantitative and qualitative analysis of type III antifreeze protein structure and function. Authors: Graether, S.P. / DeLuca, C.I. / Baardsnes, J. / Hill, G.A. / Davies, P.L. / Jia, Z. #1: 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. #2: 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. #3: 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. #4: 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. #5: 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 | 2spg.cif.gz | 23.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2spg.ent.gz | 14.9 KB | Display | PDB format |
PDBx/mmJSON format | 2spg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/2spg ftp://data.pdbj.org/pub/pdb/validation_reports/sp/2spg | HTTPS FTP |
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-Related structure data
Related structure data | 1b7iC 1b7jC 1b7kC 1eklC 1jabC 1msjC 2ameC 2jiaC 2msjC 3ameC 4ameC 6ameC 7ameC 8ameC 8msiC 9ameC 9msiC 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: 6965.207 Da / Num. of mol.: 1 / Mutation: T15S, 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: 2.13 Å3/Da / Density % sol: 42.13 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | ||||||||||||||||||||||||||||||
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: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→25 Å / Num. obs: 6388 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.079 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.35 / % possible all: 99.5 |
Reflection | *PLUS Num. measured all: 21851 / Rmerge(I) obs: 0.079 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: 1MSI Resolution: 1.75→8 Å / Cross valid method: FREE R / σ(F): 0
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Displacement parameters | Biso mean: 18.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.83 Å / Rfactor Rfree error: 0.054
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Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.348 / Rfactor Rwork: 0.29 |