+Open data
-Basic information
Entry | Database: PDB / ID: 2rjd | ||||||
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Title | Crystal structure of L3MBTL1 protein | ||||||
Components | Lethal(3)malignant brain tumor-like protein | ||||||
Keywords | TRANSCRIPTION / L(3)MBT-LIKE PROTEIN / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Alternative splicing / Chromatin regulator / DNA-binding / Metal-binding / Nucleus / Repressor / Transcription regulation / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation / heterochromatin formation ...SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation / heterochromatin formation / 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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Allali-Hassani, A. / Liu, Y. / Herzanych, N. / Ouyang, H. / Mackenzie, F. / Crombet, L. / Loppnau, P. / Kozieradzki, I. / Vedadi, M. / Weigelt, J. ...Allali-Hassani, A. / Liu, Y. / Herzanych, N. / Ouyang, H. / Mackenzie, F. / Crombet, L. / Loppnau, P. / Kozieradzki, I. / Vedadi, M. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J.R. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2007 Title: L3MBTL1 recognition of mono- and dimethylated histones. Authors: Min, J. / Allali-Hassani, A. / Nady, N. / Qi, C. / Ouyang, H. / Liu, Y. / MacKenzie, F. / Vedadi, M. / Arrowsmith, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rjd.cif.gz | 91.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rjd.ent.gz | 67 KB | Display | PDB format |
PDBx/mmJSON format | 2rjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rjd_validation.pdf.gz | 421.8 KB | Display | wwPDB validaton report |
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Full document | 2rjd_full_validation.pdf.gz | 425.9 KB | Display | |
Data in XML | 2rjd_validation.xml.gz | 19 KB | Display | |
Data in CIF | 2rjd_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/2rjd ftp://data.pdbj.org/pub/pdb/validation_reports/rj/2rjd | HTTPS FTP |
-Related structure data
Related structure data | 2pqwSC 2rjcC 2rjeC 2rjfC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37751.211 Da / Num. of mol.: 1 / Fragment: Residues 200-530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL, KIAA0681, L3MBT / Plasmid: pET28a-mhl / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y468 |
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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: 3.15 Å3/Da / Density % sol: 60.93 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 4% PEG 4000, 0.1M Sodium acetate, 1mM H1bK26me2 peptide, 0.1 M Sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 10, 2006 / Details: varimax |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→34.63 Å / Num. all: 57382 / Num. obs: 57382 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.057 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PQW Resolution: 1.65→34.63 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.744 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.093 / ESU R Free: 0.093 / 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: 29.596 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→34.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.69 Å / Total num. of bins used: 20
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