+Open data
-Basic information
Entry | Database: PDB / ID: 8hcu | ||||||
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Title | Crystal structure of BCOR/PCGF1/KDM2B complex | ||||||
Components |
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Keywords | TRANSCRIPTION / complex / PRC1 | ||||||
Function / homology | Function and homology information negative regulation of tooth mineralization / BCOR complex / specification of axis polarity / PRC1 complex / blastocyst hatching / negative regulation of bone mineralization / PcG protein complex / unmethylated CpG binding / odontogenesis / roof of mouth development ...negative regulation of tooth mineralization / BCOR complex / specification of axis polarity / PRC1 complex / blastocyst hatching / negative regulation of bone mineralization / PcG protein complex / unmethylated CpG binding / odontogenesis / roof of mouth development / heat shock protein binding / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / histone deacetylase binding / transcription corepressor activity / heart development / DNA-binding transcription factor binding / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Shen, F. / Chen, R. / Xu, J. / Liu, J. | ||||||
Funding support | China, 1items
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Citation | Journal: to be published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hcu.cif.gz | 194.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hcu.ent.gz | 153.6 KB | Display | PDB format |
PDBx/mmJSON format | 8hcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/8hcu ftp://data.pdbj.org/pub/pdb/validation_reports/hc/8hcu | 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 & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4DSN4 | ||||
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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.) Homo sapiens (human) / Gene: PCGF1, NSPC1, RNF68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BSM1 | ||||
#3: Protein | Mass: 16096.708 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCOR, KIAA1575 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6W2J9 | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å |
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: 0.9793 Å / Relative weight: 1 |
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: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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