+Open data
-Basic information
Entry | Database: PDB / ID: 3sht | ||||||
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Title | Crystal structure of human MCPH1 tandem BRCT domains | ||||||
Components | Microcephalin | ||||||
Keywords | CELL CYCLE / tandem brct domains | ||||||
Function / homology | Function and homology information regulation of chromosome condensation / neuronal stem cell population maintenance / regulation of centrosome cycle / protein localization to centrosome / establishment of mitotic spindle orientation / Condensation of Prophase Chromosomes / bone development / cerebral cortex development / mitotic cell cycle / regulation of inflammatory response ...regulation of chromosome condensation / neuronal stem cell population maintenance / regulation of centrosome cycle / protein localization to centrosome / establishment of mitotic spindle orientation / Condensation of Prophase Chromosomes / bone development / cerebral cortex development / mitotic cell cycle / regulation of inflammatory response / centrosome / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Shao, Z.H. / Li, F.D. / Yan, W. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: Specific recognition of phosphorylated tail of H2AX by the tandem BRCT domains of MCPH1 revealed by complex structure Authors: Shao, Z.H. / Li, F.D. / Sy, S.M.-H. / Yan, W. / Zhang, Z. / Gong, D. / Wen, B. / Huen, M.S.Y. / Gong, Q. / Wu, J. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sht.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sht.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 3sht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/3sht ftp://data.pdbj.org/pub/pdb/validation_reports/sh/3sht | HTTPS FTP |
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-Related structure data
Related structure data | 3shvC 2ingS 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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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 22872.615 Da / Num. of mol.: 3 / Fragment: residues 639-835 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCPH1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NEM0 #2: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE IS FROM GENBANK NP_078872.2 MICROCEPHALIN ISOFORM 1. MICROCEPHALIN HAS A NATURAL ...THIS SEQUENCE IS FROM GENBANK NP_078872.2 MICROCEPHA | |
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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: 2.87 Å3/Da / Density % sol: 57.14 % / Mosaicity: 0.171 ° |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES, 10% PEG6000, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 13, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: plane grating / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→50 Å / Num. all: 56231 / Num. obs: 54633 / % possible obs: 97.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 3.4 % / Rmerge(I) obs: 0.045 / Χ2: 0.854 / Net I/σ(I): 13.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 54.14 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ING Resolution: 1.95→32.58 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2479 / WRfactor Rwork: 0.2069 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.8311 / SU B: 3.623 / SU ML: 0.104 / SU R Cruickshank DPI: 0.1553 / SU Rfree: 0.1478 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.148 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 249.43 Å2 / Biso mean: 26.9015 Å2 / Biso min: 10 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→32.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.952→2.003 Å / Total num. of bins used: 20
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