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- PDB-4iej: Crystal structure of a DNA methyltransferase 1 associated protein... -
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Basic information
Entry | Database: PDB / ID: 4iej | ||||||
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Title | Crystal structure of a DNA methyltransferase 1 associated protein 1 (DMAP1) from Homo sapiens at 1.45 A resolution | ||||||
![]() | DNA methyltransferase 1-associated protein 1 | ||||||
![]() | TRANSCRIPTION / DNA methylation / chromatin regulator / repressor / Structural Genomics / Joint Center for Structural Genomics / JCSG / Partnership for T-Cell Biology / TCELL / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | ![]() Swr1 complex / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / replication fork / positive regulation of protein import into nucleus / transcription corepressor activity / nucleosome / HATs acetylate histones / regulation of apoptotic process ...Swr1 complex / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / replication fork / positive regulation of protein import into nucleus / transcription corepressor activity / nucleosome / HATs acetylate histones / regulation of apoptotic process / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / regulation of cell cycle / chromatin remodeling / DNA repair / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL) | ||||||
![]() | ![]() Title: Crystal structure of a DNA methyltransferase 1 associated protein 1 (DMAP1) from Homo sapiens at 1.45 A resolution Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.9 KB | Display | ![]() |
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PDB format | ![]() | 36.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.4 KB | Display | ![]() |
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Full document | ![]() | 417.4 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Data in CIF | ![]() | 7.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hm5S S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11216.549 Da / Num. of mol.: 1 / Fragment: SANT domain containing residues 121-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Sequence details | THE CONSTRUCT (121-212) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (121-212) WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.20M calcium chloride 20.00% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2012 Details: Rhodium-coated vertical and horizontal focusing mirrors, liquid-nitrogen cooled double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→38.327 Å / Num. obs: 18199 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.311 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.99 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3hm5 Resolution: 1.45→38.327 Å / Cor.coef. Fo:Fc: 0.9512 / Cor.coef. Fo:Fc free: 0.9482 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. CALCIUM ION MODELED IS PRESENT IN CRYSTALLIZATION BUFFER.
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Displacement parameters | Biso max: 112.38 Å2 / Biso mean: 36.2049 Å2 / Biso min: 17.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.251 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→38.327 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.54 Å / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: 4.3298 Å / Origin y: 24.2719 Å / Origin z: 6.973 Å
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Refinement TLS group | Selection details: { A|133 - A|207 } |