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Open data
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Basic information
Entry | Database: PDB / ID: 8hcu | ||||||
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Title | Crystal structure of BCOR/PCGF1/KDM2B complex | ||||||
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Function / homology | ![]() negative regulation of tooth mineralization / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Shen, F. / Chen, R. / Xu, J. / Liu, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of BCOR/PCGF1/KDM2B complex Authors: Shen, F. / Chen, R. / Xu, J. / Liu, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.9 KB | Display | ![]() |
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PDB format | ![]() | 153.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4hplS ![]() 5jh5S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26469.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 12636.700 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
#3: Protein | ![]() Mass: 16096.708 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
#4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % / Mosaicity: 0.14 ° |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion / pH: 6.2 Details: 0.1M magnesium acetate, 0.1M sodium citrate pH6.2, 4% PEG5000MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→126.02 Å / Num. obs: 30637 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.033 / Rrim(I) all: 0.122 / Χ2: 1.02 / Net I/σ(I): 12 / Num. measured all: 421860 |
Reflection shell | Resolution: 2.2→2.27 Å / % possible obs: 99.9 % / Redundancy: 14.6 % / Rmerge(I) obs: 1.218 / Num. measured all: 37997 / Num. unique obs: 2605 / CC1/2: 0.936 / Rpim(I) all: 0.329 / Rrim(I) all: 1.262 / Χ2: 1.04 / Net I/σ(I) obs: 2.4 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5JH5, 4HPL Resolution: 2.2→65.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 15.499 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.188 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.831 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→65.01 Å
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Refine LS restraints |
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