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- PDB-2ri2: Crystal structure of the 3-MBT repeats from human L3MBTL1 with D3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ri2 | ||||||
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Title | Crystal structure of the 3-MBT repeats from human L3MBTL1 with D355A point mutation | ||||||
![]() | Lethal(3)malignant brain tumor-like protein | ||||||
![]() | TRANSCRIPTION / beta barrel / 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 / heterochromatin formation / nucleosome binding / 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 / heterochromatin formation / nucleosome binding / 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 | ![]() | ||||||
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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.8 KB | Display | ![]() |
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PDB format | ![]() | 64 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.3 KB | Display | ![]() |
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Full document | ![]() | 461.2 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 26.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rhiC ![]() 2rhuC ![]() 2rhxC ![]() 2rhySC ![]() 2rhzC ![]() 2ri3C ![]() 2ri5C ![]() 2ri7C 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
#1: Protein | Mass: 36649.949 Da / Num. of mol.: 1 / Fragment: Repeates MBT-1, MBT-2, MBT-3; residues 206-519 / Mutation: D355A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5% PEG10K, 0.1 M Tris-maleate pH 6.5, 0.1 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 30, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 24392 / Num. obs: 23416 / % possible obs: 96 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 4.9 / Num. unique all: 2330 / Rsym value: 0.568 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2RHY Resolution: 2.2→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: 42.1 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å
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