+Open data
-Basic information
Entry | Database: PDB / ID: 6jk4 | ||||||
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Title | Ca2+-dependent type II antifreeze protein | ||||||
Components | Type II antifreeze protein | ||||||
Keywords | ANTIFREEZE PROTEIN / C-type lectin / ice-binding protein | ||||||
Function / homology | Function and homology information Type-2 ice-structuring protein / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily ...Type-2 ice-structuring protein / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Hypomesus nipponensis (Japanese smelt) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å | ||||||
Authors | Arai, T. / Tsuda, S. / Kondo, H. / Nishimiya, Y. | ||||||
Citation | Journal: Biomolecules / Year: 2019 Title: Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface. Authors: Arai, T. / Nishimiya, Y. / Ohyama, Y. / Kondo, H. / Tsuda, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jk4.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jk4.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/6jk4 ftp://data.pdbj.org/pub/pdb/validation_reports/jk/6jk4 | HTTPS FTP |
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-Related structure data
Related structure data | 6jk5C 2zibS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15321.056 Da / Num. of mol.: 1 / Mutation: N12D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hypomesus nipponensis (Japanese smelt) / Plasmid: pPICZalpha / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: P84493 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.1 M sodium acetate, 0.25 M ammonium sulfate, 8% PEG 3350 The Crystal was soaked in crystallizaion solution containing 2mM CaCl2 and pH adjusted to 7.0 before data collection. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 29, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→21.567 Å / Num. obs: 56672 / % possible obs: 99.7 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.048 / Rsym value: 0.045 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.06→1.12 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 8207 / Rrim(I) all: 0.241 / Rsym value: 0.229 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZIB Resolution: 1.06→19.04 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.324 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.774 Å2
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Refinement step | Cycle: 1 / Resolution: 1.06→19.04 Å
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Refine LS restraints |
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