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Yorodumi- PDB-4to7: N-Terminal domain of C. Reinhardtii SAS-6 homolog bld12p Q93E F14... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4to7 | ||||||
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Title | N-Terminal domain of C. Reinhardtii SAS-6 homolog bld12p Q93E F145W K146R (NN24) | ||||||
Components | Centriole protein | ||||||
Keywords | STRUCTURAL PROTEIN / SAS-6 / cartwheel | ||||||
Function / homology | Spindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal domain / centriole / cell cycle / identical protein binding / cytoplasm / Centriole protein Function and homology information | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.252 Å | ||||||
Authors | Hilbert, M. / Kraatz, S.H.W. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Nat.Cell Biol. / Year: 2016 Title: SAS-6 engineering reveals interdependence between cartwheel and microtubules in determining centriole architecture. Authors: Hilbert, M. / Noga, A. / Frey, D. / Hamel, V. / Guichard, P. / Kraatz, S.H. / Pfreundschuh, M. / Hosner, S. / Fluckiger, I. / Jaussi, R. / Wieser, M.M. / Thieltges, K.M. / Deupi, X. / ...Authors: Hilbert, M. / Noga, A. / Frey, D. / Hamel, V. / Guichard, P. / Kraatz, S.H. / Pfreundschuh, M. / Hosner, S. / Fluckiger, I. / Jaussi, R. / Wieser, M.M. / Thieltges, K.M. / Deupi, X. / Muller, D.J. / Kammerer, R.A. / Gonczy, P. / Hirono, M. / Steinmetz, M.O. #1: Journal: Cell / Year: 2011 Title: Structural basis of the 9-fold symmetry of centrioles. Authors: Kitagawa, D. / Vakonakis, I. / Olieric, N. / Hilbert, M. / Keller, D. / Olieric, V. / Bortfeld, M. / Erat, M.C. / Flueckiger, I. / Goenczy, P. / Steinmetz, M.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4to7.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4to7.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 4to7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4to7_validation.pdf.gz | 423.7 KB | Display | wwPDB validaton report |
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Full document | 4to7_full_validation.pdf.gz | 424 KB | Display | |
Data in XML | 4to7_validation.xml.gz | 9 KB | Display | |
Data in CIF | 4to7_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/4to7 ftp://data.pdbj.org/pub/pdb/validation_reports/to/4to7 | HTTPS FTP |
-Related structure data
Related structure data | 4tpzC 4tq7C 4ttwC 4ttxC 4ttyC 4ttzC 4u2iC 4u2jC 3qoyS 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: 18171.654 Da / Num. of mol.: 1 / Mutation: Q93E, K146R, F145W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CrSAS-6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CQL4 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.98 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.5 / Details: PEG3350, MES-NaOH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→52.1 Å / Num. obs: 41536 / % possible obs: 98.7 % / Redundancy: 12.4 % / Net I/σ(I): 17.42 |
Reflection shell | Resolution: 1.25→1.28 Å / Redundancy: 12 % / Rmerge(I) obs: 5.916 / Mean I/σ(I) obs: 0.44 / % possible all: 84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3qoy Resolution: 1.252→19.66 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.49 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.252→19.66 Å
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Refine LS restraints |
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LS refinement shell |
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