+Open data
-Basic information
Entry | Database: PDB / ID: 7kyq | ||||||
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Title | Crystal structure of human BCCIP beta (Native1) | ||||||
Components | BRCA2 and CDKN1A-interacting protein | ||||||
Keywords | TRANSFERASE / BRCA2 / eIF6 / cancer suppressor / ribosome biogenesis / GNAT / GCN5-related acetyltransferase | ||||||
Function / homology | Function and homology information microtubule anchoring / nuclear cyclin-dependent protein kinase holoenzyme complex / neuroendocrine cell differentiation / kinase regulator activity / regulation of cyclin-dependent protein serine/threonine kinase activity / mitotic spindle pole / establishment of mitotic spindle orientation / mitotic spindle assembly / centriole / tubulin binding ...microtubule anchoring / nuclear cyclin-dependent protein kinase holoenzyme complex / neuroendocrine cell differentiation / kinase regulator activity / regulation of cyclin-dependent protein serine/threonine kinase activity / mitotic spindle pole / establishment of mitotic spindle orientation / mitotic spindle assembly / centriole / tubulin binding / mitotic spindle organization / microtubule cytoskeleton organization / DNA repair / centrosome / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.06 Å | ||||||
Authors | Choi, W.S. / Liu, B. / Shen, Z. / Yang, W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2021 Title: Structure of human BCCIP and implications for binding and modification of partner proteins. Authors: Choi, W.S. / Liu, B. / Shen, Z. / Yang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kyq.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kyq.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 7kyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kyq_validation.pdf.gz | 427 KB | Display | wwPDB validaton report |
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Full document | 7kyq_full_validation.pdf.gz | 434.5 KB | Display | |
Data in XML | 7kyq_validation.xml.gz | 12 KB | Display | |
Data in CIF | 7kyq_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/7kyq ftp://data.pdbj.org/pub/pdb/validation_reports/ky/7kyq | HTTPS FTP |
-Related 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: 29282.535 Da / Num. of mol.: 1 / Fragment: UNP residues 61-314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCCIP, TOK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9P287, Transferases |
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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: 3.08 Å3/Da / Density % sol: 60.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M tri-sodium citrate, 18-20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 17, 2019 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.04→40 Å / Num. obs: 7295 / % possible obs: 99.8 % / Redundancy: 12.4 % / Biso Wilson estimate: 85.03 Å2 / CC1/2: 0.995 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 3.04→3.09 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 341 / CC1/2: 0.911 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.06→39.84 Å / SU ML: 0.3649 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.1879 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.06→39.84 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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