+Open data
-Basic information
Entry | Database: PDB / ID: 3k9k | ||||||
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Title | Transposase domain of Metnase | ||||||
Components | Histone-lysine N-methyltransferase SETMAR | ||||||
Keywords | TRANSFERASE / transposase / Chromatin regulator / DNA damage / DNA repair / DNA-binding / Methyltransferase / Nucleus / Phosphoprotein | ||||||
Function / homology | Function and homology information negative regulation of chromosome organization / mitotic DNA integrity checkpoint signaling / [histone H3]-lysine36 N-dimethyltransferase / DNA topoisomerase binding / histone H3K36 dimethyltransferase activity / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / nucleic acid metabolic process / single-stranded DNA endodeoxyribonuclease activity / DNA double-strand break processing / histone H3K36 methyltransferase activity ...negative regulation of chromosome organization / mitotic DNA integrity checkpoint signaling / [histone H3]-lysine36 N-dimethyltransferase / DNA topoisomerase binding / histone H3K36 dimethyltransferase activity / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / nucleic acid metabolic process / single-stranded DNA endodeoxyribonuclease activity / DNA double-strand break processing / histone H3K36 methyltransferase activity / DNA catabolic process / histone H3K4 methyltransferase activity / replication fork processing / positive regulation of double-strand break repair via nonhomologous end joining / DNA integration / double-strand break repair via nonhomologous end joining / site of double-strand break / single-stranded DNA binding / methylation / double-stranded DNA binding / endonuclease activity / cell population proliferation / Hydrolases; Acting on ester bonds / nucleolus / protein homodimerization activity / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Goodwin, K.D. / He, H. / Imasaki, T. / Lee, S.-H. / Georgiadis, M.M. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Crystal structure of the human Hsmar1-derived transposase domain in the DNA repair enzyme Metnase. Authors: Goodwin, K.D. / He, H. / Imasaki, T. / Lee, S.H. / Georgiadis, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k9k.cif.gz | 100.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k9k.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 3k9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/3k9k ftp://data.pdbj.org/pub/pdb/validation_reports/k9/3k9k | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 28535.418 Da / Num. of mol.: 2 / Mutation: N566R, G569R, A649W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETMAR / Plasmid: pET15b / Production host: Escherichia coli (E. coli) References: UniProt: Q53H47, histone-lysine N-methyltransferase #2: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE DNA USED FOR THE STUDIES ENCODES A GLU FOR POSITION 438, WHICH MIGHT BE A ...AUTHORS STATE THAT THE DNA USED FOR THE STUDIES ENCODES A GLU FOR POSITION 438, WHICH MIGHT BE A NATURAL VARIANT. | |
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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: 2.52 Å3/Da / Density % sol: 51.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: NH4OAc, CaCl2, PEG4000, pH 8.0, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.107203 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2007 |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal monochromator, LN2 cooled first crystal, sagittal focusing 2nd crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.107203 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 20325 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.058 / Rsym value: 0.039 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.727 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→35.872 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 2.43 / σ(F): 1 / Phase error: 30.11 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.344 Å2 / ksol: 0.333 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.55→35.872 Å
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Refine LS restraints |
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LS refinement shell |
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Xplor file |
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