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Yorodumi- PDB-4bxq: Structure of the E1021V mutant of the TCP10 domain of Danio rerio CPAP -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bxq | ||||||
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Title | Structure of the E1021V mutant of the TCP10 domain of Danio rerio CPAP | ||||||
Components | CPAPContinuous positive airway pressure | ||||||
Keywords | CELL CYCLE / CENTRIOLE DUPLICATION | ||||||
Function / homology | Function and homology information TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of mitotic spindle organization / : / : / : / : / Anchoring of the basal body to the plasma membrane / : / centriole elongation / Regulation of PLK1 Activity at G2/M Transition ...TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of mitotic spindle organization / : / : / : / : / Anchoring of the basal body to the plasma membrane / : / centriole elongation / Regulation of PLK1 Activity at G2/M Transition / procentriole replication complex / positive regulation of centriole replication / positive regulation of spindle assembly / cilium assembly / positive regulation of G1/S transition of mitotic cell cycle / centriole / tubulin binding / protein domain specific binding / centrosome / cytoplasm Similarity search - Function | ||||||
Biological species | DANIO RERIO (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | van Breugel, M. | ||||||
Citation | Journal: Elife / Year: 2013 Title: Crystal structures of the CPAP/STIL complex reveal its role in centriole assembly and human microcephaly. Authors: Cottee, M.A. / Muschalik, N. / Wong, Y.L. / Johnson, C.M. / Johnson, S. / Andreeva, A. / Oegema, K. / Lea, S.M. / Raff, J.W. / van Breugel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bxq.cif.gz | 51 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bxq.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/4bxq ftp://data.pdbj.org/pub/pdb/validation_reports/bx/4bxq | HTTPS FTP |
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-Related structure data
Related structure data | 4bxpSC 4bxrC 4by2C 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
#1: Protein | Mass: 21861.557 Da / Num. of mol.: 1 / Fragment: TCP-10 DOMAIN, RESIDUE 937-1124 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: E7FCY1 |
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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: 2.18 Å3/Da / Density % sol: 43.6 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 80 MM TRIS PH 8.5, 160 MM MGCL2, 24% PEG-4000, 20% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 11, 2010 / Details: MULTILAYER FOCUSSING OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→36.5 Å / Num. obs: 15136 / % possible obs: 100 % / Observed criterion σ(I): 1.8 / Redundancy: 6.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BXP Resolution: 1.9→29.49 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.329 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.168 / 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 mean: 31.553 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.49 Å
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