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Yorodumi- PDB-1oyx: CRYSTAL STRUCTURE OF 3-MBT REPEATS OF LETHAL (3) MALIGNANT BRAIN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oyx | ||||||
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Title | CRYSTAL STRUCTURE OF 3-MBT REPEATS OF LETHAL (3) MALIGNANT BRAIN TUMOR (SELENO-MET) AT 1.85 ANGSTROM | ||||||
Components | Lethal(3)malignant brain tumor-like protein | ||||||
Keywords | TRANSCRIPTION / propeller / transcription repressor | ||||||
Function / homology | Function and homology information SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / heterochromatin formation / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation ...SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / heterochromatin formation / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation / chromatin organization / histone binding / regulation of cell cycle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / zinc ion binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å | ||||||
Authors | Wang, W.K. / Tereshko, V. / Boccuni, P. / MacGrogan, D. / Nimer, S.D. / Patel, D.J. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Malignant brain tumor repeats: a three-leaved propeller architecture with ligand/peptide binding pockets. Authors: Wang, W.K. / Tereshko, V. / Boccuni, P. / MacGrogan, D. / Nimer, S.D. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oyx.cif.gz | 211.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oyx.ent.gz | 176.6 KB | Display | PDB format |
PDBx/mmJSON format | 1oyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/1oyx ftp://data.pdbj.org/pub/pdb/validation_reports/oy/1oyx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a trimer generated by the operations: -y, x-y, z+2/3, -x+y, -x, z+1/3 |
-Components
#1: Protein | Mass: 38043.758 Da / Num. of mol.: 3 / Fragment: residues 197-527 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: brain / Gene: L3MBTL OR L3MBT OR KIAA0681 / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE(3)RP / References: UniProt: Q9Y468 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MES / #4: 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: 2.55 Å3/Da / Density % sol: 51.75 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG MME 5000, MES, DTT, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.06334, 0.97935, 0.97914, 0.95668 | |||||||||||||||
Detector | Detector: CCD / Date: Sep 15, 2002 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→20 Å / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.059 | |||||||||||||||
Reflection shell | Resolution: 1.85→1.9 Å / Rmerge(I) obs: 0.55 / Num. unique all: 4088 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 88637 / % possible obs: 97 % | |||||||||||||||
Reflection shell | *PLUS % possible obs: 94.2 % / Num. unique obs: 4088 / Rmerge(I) obs: 0.55 |
-Processing
Software |
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Refinement | Resolution: 1.85→19.84 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.968 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.153 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 31.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 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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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 1.9 Å / Rfactor Rfree: 0.53 |