+Open data
-Basic information
Entry | Database: PDB / ID: 3boi | ||||||
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Title | Snow Flea Antifreeze Protein Racemate | ||||||
Components | 6.5 kDa glycine-rich antifreeze protein | ||||||
Keywords | ANTIFREEZE PROTEIN / racemate / sfAFP / mirror image proteins / racemic protein crystallography | ||||||
Function / homology | 6.5 kDa glycine-rich antifreeze protein Function and homology information | ||||||
Biological species | Hypogastrura harveyi (arthropod) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1 Å | ||||||
Authors | Pentelute, B.L. / Kent, S.B.H. / Gates, Z.P. / Tereshko, V. / Kossiakoff, A.A. / Kurutz, J. / Dashnau, J. / Vaderkooi, J.M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2008 Title: X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers Authors: Pentelute, B.L. / Gates, Z.P. / Tereshko, V. / Dashnau, J.L. / Vanderkooi, J.M. / Kossiakoff, A.A. / Kent, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3boi.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3boi.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 3boi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/3boi ftp://data.pdbj.org/pub/pdb/validation_reports/bo/3boi | HTTPS FTP |
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-Related structure data
Related structure data | 2pneC 3bogC 3b0gS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6489.812 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The protein was chemically synthesized. / Source: (synth.) Hypogastrura harveyi (arthropod) / References: UniProt: Q38PT6 #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: 2.05 Å3/Da / Density % sol: 40.1 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97918 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 7, 2007 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→50 Å / Num. obs: 101192 / % possible obs: 78.2 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 0.95→0.98 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.6 / % possible all: 18.9 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 3B0G Resolution: 1→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.948 / SU B: 0.327 / SU ML: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1→1.03 Å / Total num. of bins used: 20
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