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- PDB-7ddb: Crystal structure of fungal antifreeze protein with intermediate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ddb | ||||||
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Title | Crystal structure of fungal antifreeze protein with intermediate activity | ||||||
![]() | Antifreeze protein | ||||||
![]() | ANTIFREEZE PROTEIN / right-handed beta-helix / beta-solenoid / ice-binding protein / thermal hysteresis protein / ice-structuring protein | ||||||
Function / homology | Ice-binding protein / Ice-binding-like / Antifreeze protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Khan, N.M.M.U. / Arai, T. / Tsuda, S. / Kondo, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Characterization of microbial antifreeze protein with intermediate activity suggests that a bound-water network is essential for hyperactivity. Authors: Khan, N.M.U. / Arai, T. / Tsuda, S. / Kondo, 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 | ![]() | 104.6 KB | Display | ![]() |
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PDB format | ![]() | 77 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.7 KB | Display | ![]() |
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Full document | ![]() | 423.6 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dc5C ![]() 5b5hS C: citing same article ( 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22089.811 Da / Num. of mol.: 2 / Mutation: T20Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.65 % / Description: thin plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl pH8.5, 30% (w/v) PEG 4000, 0.2M magnesium chloride PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 17, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→49.68 Å / Num. obs: 41109 / % possible obs: 99.8 % / Redundancy: 12.9 % / CC1/2: 0.98 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.057 / Rrim(I) all: 0.201 / Net I/σ(I): 8.6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5B5H Resolution: 1.72→49.68 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.005 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1457 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.39 Å2 / Biso mean: 10.893 Å2 / Biso min: 2.36 Å2
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Refinement step | Cycle: final / Resolution: 1.72→49.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.765 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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