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Yorodumi- PDB-3ktf: Structure of the N-terminal BRCT domain of human microcephalin (M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ktf | ||||||
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Title | Structure of the N-terminal BRCT domain of human microcephalin (MCPH1). | ||||||
Components | Microcephalin | ||||||
Keywords | CELL CYCLE / BRCT DOMAIN / MCPH1 / MICROCEPHALIN / Cytoplasm / Cytoskeleton / Dwarfism / Mental retardation / Phosphoprotein / Polymorphism / Primary microcephaly | ||||||
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 / SAD / Resolution: 1.6 Å | ||||||
Authors | Singh, N. / Heroux, A. / Thompson, J.R. / Mer, G. | ||||||
Citation | Journal: To be Published Title: Structure of N-terminal BRCT domain of human microcephalin (MCPH1) Authors: Singh, N. / Heroux, A. / Thompson, J.R. / Mer, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ktf.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ktf.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ktf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ktf_validation.pdf.gz | 415.7 KB | Display | wwPDB validaton report |
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Full document | 3ktf_full_validation.pdf.gz | 419 KB | Display | |
Data in XML | 3ktf_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 3ktf_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/3ktf ftp://data.pdbj.org/pub/pdb/validation_reports/kt/3ktf | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 11644.769 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCPH1 / Plasmid: pGB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NEM0 #2: Chemical | ChemComp-CL / | #3: 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: 2.1 Å3/Da / Density % sol: 41.47 % |
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Crystal grow | Temperature: 295 K / pH: 7 Details: 0.2M sodium succinate, 15% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979095 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2008 |
Radiation | Monochromator: SI(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979095 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 36909 / % possible obs: 88.9 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 46.07 |
Reflection shell | Resolution: 1.55→1.62 Å / Redundancy: 4 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.95 / % possible all: 64.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.387 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.083 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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