+Open data
-Basic information
Entry | Database: PDB / ID: 3msi | ||||||
---|---|---|---|---|---|---|---|
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 / Resolution: 1.43 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3msi.cif.gz | 21.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3msi.ent.gz | 15.8 KB | Display | PDB format |
PDBx/mmJSON format | 3msi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/3msi ftp://data.pdbj.org/pub/pdb/validation_reports/ms/3msi | HTTPS FTP |
---|
-Related structure data
Related structure data | 2msiC 4msiC 5msiC 6msiC 7msiC 1msiS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 7063.395 Da / Num. of mol.: 1 / Mutation: A16H 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 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Details: PROTEIN WAS CRYSTALLIZED IN 50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5 | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 30 % | ||||||||||||||||||||||||||||||
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
|
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 11, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→8 Å / Num. obs: 4933 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rsym value: 0.077 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Rsym value: 0.306 / % possible all: 98.3 |
Reflection | *PLUS Highest resolution: 1.43 Å / Num. obs: 9650 / % possible obs: 83.9 % / Num. measured all: 40197 / Rmerge(I) obs: 0.065 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: 1MSI Resolution: 1.43→50 Å / Cross valid method: FREE-R REFINEMENT / σ(F): 1
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→50 Å
| ||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Num. reflection obs: 9650 / Rfactor obs: 0.191 / Rfactor Rfree: 0.25 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |