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- PDB-2rhx: Crystal structure of the 3-MBT repeats from human L3MBTL1 bound t... -
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Basic information
Entry | Database: PDB / ID: 2rhx | ||||||
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Title | Crystal structure of the 3-MBT repeats from human L3MBTL1 bound to dimethyl-lysine | ||||||
![]() | Lethal(3)malignant brain tumor-like protein | ||||||
![]() | TRANSCRIPTION / Beta Barrel / dimethyl-lysine / Alternative splicing / Chromatin regulator / DNA-binding / Metal-binding / Nucleus / Repressor / Transcription regulation / Zinc / Zinc-finger | ||||||
Function / homology | ![]() SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / condensed chromosome / : / 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 / : / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, H. / Patel, D.J. | ||||||
![]() | ![]() Title: Structural Basis for Lower Lysine Methylation State-Specific Readout by MBT Repeats of L3MBTL1 and an Engineered PHD Finger. Authors: Li, H. / Fischle, W. / Wang, W. / Duncan, E.M. / Liang, L. / Murakami-Ishibe, S. / Allis, C.D. / Patel, D.J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.6 KB | Display | ![]() |
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PDB format | ![]() | 65.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 469.2 KB | Display | ![]() |
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Full document | ![]() | 470.5 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rhiC ![]() 2rhuC ![]() 2rhyC ![]() 2rhzC ![]() 2ri2C ![]() 2ri3C ![]() 2ri5C ![]() 2ri7C ![]() 1oz2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39195.727 Da / Num. of mol.: 1 / Fragment: Repeates MBT-1, MBT-2, MBT-3; residues 197-526 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 311 molecules 








#2: Chemical | #3: Chemical | ChemComp-MLY / | #4: Chemical | ChemComp-PG4 / | #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Crystals of the Kme2-L3MBTL1(197-526) complex were generated by pre-incubating L3MBTL1 (17MG/ML IN 50MM KCL, 25MM TRIS-HCL PH 8.0, 1MM DTT) with a five-fold molar excess of dimethyl-lysine ...Details: Crystals of the Kme2-L3MBTL1(197-526) complex were generated by pre-incubating L3MBTL1 (17MG/ML IN 50MM KCL, 25MM TRIS-HCL PH 8.0, 1MM DTT) with a five-fold molar excess of dimethyl-lysine amino acid. Drops were prepared by mixing equal volumes of the complex with reservoir solution (0.1 M bis-Tris, pH 6.5, 15% PEG MME 5000, 0.15 M ammonium sulfate, and 10 mM DTT)., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 28527 / Num. obs: 28356 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2800 / Rsym value: 0.572 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OZ2 Resolution: 2.1→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 38 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.17 Å
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