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Yorodumi- PDB-6zq3: Crystal Structure of Silicatein Alpha from Marine Sponge Tethya a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zq3 | ||||||
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Title | Crystal Structure of Silicatein Alpha from Marine Sponge Tethya aurantium | ||||||
Components | Silicatein alpha | ||||||
Keywords | HYDROLASE / Silica / Silicatein / Sponges / Demosponges / Spicules | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Tethya aurantium (orange puffball sponge) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Goerlich, S. / Leonarski, R.J. / Tomizaki, T. / Zlotnikov, I. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Natural hybrid silica/protein superstructure at atomic resolution. Authors: Gorlich, S. / Samuel, A.J. / Best, R.J. / Seidel, R. / Vacelet, J. / Leonarski, F.K. / Tomizaki, T. / Rellinghaus, B. / Pohl, D. / Zlotnikov, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zq3.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zq3.ent.gz | 37.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/6zq3 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/6zq3 | HTTPS FTP |
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-Related structure data
Related structure data | 2vhsS S: Starting model for refinement |
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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
#1: Protein | Mass: 23292.543 Da / Num. of mol.: 1 / Fragment: mature enzyme / Source method: isolated from a natural source / Details: tissue / Source: (natural) Tethya aurantium (orange puffball sponge) / References: UniProt: O76238 |
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#2: 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: 2.56 Å3/Da / Density % sol: 51.95 % |
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Crystal grow | Temperature: 298 K / Method: in cell / Details: in vivo |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2019 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→51.5 Å / Num. obs: 9827 / % possible obs: 100 % / Redundancy: 159 % / CC1/2: 0.91 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.4→2.486 Å / Num. unique obs: 973 / CC1/2: 0.58 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdbid 2VHS Resolution: 2.4→47.18 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.7 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.39 / ESU R Free: 0.295 / 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: 95.98 Å2 / Biso mean: 49.104 Å2 / Biso min: 35.2 Å2
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Refinement step | Cycle: final / Resolution: 2.4→47.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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