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Yorodumi- PDB-4ke2: Crystal structure of the hyperactive Type I antifreeze from winte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ke2 | ||||||
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Title | Crystal structure of the hyperactive Type I antifreeze from winter flounder | ||||||
Components | Type I hyperactive antifreeze protein | ||||||
Keywords | ANTIFREEZE PROTEIN / dimeric alpha-helical bundle | ||||||
Function / homology | Helix Hairpins - #1860 / Antifreeze protein, type I / ice binding / Helix Hairpins / Helix non-globular / Special / extracellular region / identical protein binding / Antifreeze protein Maxi Function and homology information | ||||||
Biological species | Pseudopleuronectes americanus (winter flounder) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | ||||||
Authors | Sun, T. / Lin, F.-H. / Campbell, R.L. / Allingham, J.S. / Davies, P.L. | ||||||
Citation | Journal: Science / Year: 2014 Title: An antifreeze protein folds with an interior network of more than 400 semi-clathrate waters. Authors: Sun, T. / Lin, F.H. / Campbell, R.L. / Allingham, J.S. / Davies, P.L. #1: Journal: J.Biol.Chem. / Year: 2005 Title: Hyperactive antifreeze protein from winter flounder is a very long rod-like dimer of alpha-helices. Authors: Marshall, C.B. / Chakrabartty, A. / Davies, P.L. #2: Journal: Biochemistry / Year: 2008 Title: Hyperactive antifreeze protein from fish contains multiple ice-binding sites. Authors: Graham, L.A. / Marshall, C.B. / Lin, F.H. / Campbell, R.L. / 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 | 4ke2.cif.gz | 217.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ke2.ent.gz | 178.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ke2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ke2_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 4ke2_full_validation.pdf.gz | 434.5 KB | Display | |
Data in XML | 4ke2_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 4ke2_validation.cif.gz | 65.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/4ke2 ftp://data.pdbj.org/pub/pdb/validation_reports/ke/4ke2 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16825.670 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: deleted signal sequence Source: (gene. exp.) Pseudopleuronectes americanus (winter flounder) Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1P0S1 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.17 Å3/Da / Density % sol: 70.49 % |
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Crystal grow | Temperature: 277 K / pH: 9.6 Details: 0.2 M NaSCN, 12.5% PEG 3350, 100mM Arginine, pH 9.6, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9788 |
Detector | Type: ADSC Q270 / Detector: CCD / Date: Jul 11, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: MIR / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 77118 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.64 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.225 / Mean I/σ(I) obs: 1.77 / % possible all: 98.6 |
-Phasing
Phasing | Method: MIR |
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-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→47.88 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.23 / Isotropic thermal model: isotropic / σ(F): 0 / Phase error: 28.25 / Stereochemistry target values: ML
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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: 23.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→47.88 Å
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Refine LS restraints |
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LS refinement shell |
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