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- PDB-6a8k: Crystal structure of Ice-binding Protein from a Sea-Ice Microalga -
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Open data
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Basic information
Entry | Database: PDB / ID: 6a8k | ||||||
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Title | Crystal structure of Ice-binding Protein from a Sea-Ice Microalga | ||||||
![]() | Ice binding protein 1 | ||||||
![]() | ANTIFREEZE PROTEIN / beta-solenoid right-handed beta-helix | ||||||
Function / homology | Ice-binding protein / Ice-binding-like / Ice binding protein 1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kondo, H. / Bayer-Giraldi, M. | ||||||
![]() | ![]() Title: Multiple binding modes of a moderate ice-binding protein from a polar microalga Authors: Kondo, H. / Mochizuki, K. / Bayer-Giraldi, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.9 KB | Display | ![]() |
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PDB format | ![]() | 46.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 728 KB | Display | ![]() |
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Full document | ![]() | 731 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vn3S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 25956.189 Da / Num. of mol.: 1 / Fragment: UNP residues 42-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Sequence details | AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS DR026070 FOR THIS SEQUENCE. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl pH8.5, 2.0M Ammonium dihydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→47.6 Å / Num. obs: 46394 / % possible obs: 99.7 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 6.3 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VN3 Resolution: 1.4→47.59 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.789 / SU ML: 0.031 / Cross valid method: FREE R-VALUE / ESU R: 0.047 / ESU R Free: 0.05 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.013 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→47.59 Å
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Refine LS restraints |
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