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Open data
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Basic information
Entry | Database: PDB / ID: 7ehk | ||||||
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Title | Crystal structure of C107S mutant of FfIBP | ||||||
![]() | Ice-binding protein | ||||||
![]() | ANTIFREEZE PROTEIN / ice-binding protein / capping head region | ||||||
Function / homology | Ice-binding protein / Ice-binding-like / extracellular region / Ice-binding protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Do, H. / Lee, J.H. | ||||||
![]() | ![]() Title: Importance of rigidity of ice-binding protein (FfIBP) for hyperthermal hysteresis activity and microbial survival. Authors: Hwang, J. / Kim, B. / Lee, M.J. / Kim, E.J. / Cho, S.M. / Lee, S.G. / Han, S.J. / Kim, K. / Lee, J.H. / Do, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.4 KB | Display | ![]() |
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PDB format | ![]() | 38.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.7 KB | Display | ![]() |
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Full document | ![]() | 428.4 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nu2S 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: 25714.855 Da / Num. of mol.: 1 / Mutation: C107S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium acetate pH 4.6, 3M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.4 Å / Num. obs: 30586 / % possible obs: 99.9 % / Redundancy: 26.2 % / Biso Wilson estimate: 44.88 Å2 / CC1/2: 0.99 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 2213 / CC1/2: 0.96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NU2 Resolution: 2→29.4 Å / SU ML: 0.2886 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.9264 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.4 Å
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Refine LS restraints |
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LS refinement shell |
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