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Yorodumi- PDB-1g55: Structure of human DNMT2, an enigmatic DNA methyltransferase homologue -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g55 | ||||||
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Title | Structure of human DNMT2, an enigmatic DNA methyltransferase homologue | ||||||
Components | DNA CYTOSINE METHYLTRANSFERASE DNMT2 | ||||||
Keywords | TRANSFERASE / Human DNA Methyltransferase homologue | ||||||
Function / homology | Function and homology information tRNA (cytosine38-C5)-methyltransferase / tRNA stabilization / tRNA methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / tRNA modification in the nucleus and cytosol / tRNA modification / tRNA methylation / response to amphetamine / RNA binding / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | ||||||
Authors | Dong, A. / Yoder, J.A. / Zhang, X. / Zhou, L. / Bestor, T.H. / Cheng, X. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2001 Title: Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA. Authors: Dong, A. / Yoder, J.A. / Zhang, X. / Zhou, L. / Bestor, T.H. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g55.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g55.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 1g55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g55_validation.pdf.gz | 485.1 KB | Display | wwPDB validaton report |
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Full document | 1g55_full_validation.pdf.gz | 487.5 KB | Display | |
Data in XML | 1g55_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 1g55_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/1g55 ftp://data.pdbj.org/pub/pdb/validation_reports/g5/1g55 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39276.371 Da / Num. of mol.: 1 / Mutation: DELETION (RESIDUES 191-237) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: O14717, DNA (cytosine-5-)-methyltransferase |
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-Non-polymers , 5 types, 260 molecules
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-SAH / |
#4: Chemical | ChemComp-BME / |
#5: Chemical | ChemComp-GOL / |
#6: 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: 3.01 Å3/Da / Density % sol: 59.18 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.3-1.4 M ammonium sulfate, 8 % glycerol, 100 mM glycine-NaOH pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→20 Å / Num. all: 41963 / Num. obs: 146987 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.4 | ||||||||||||||||||||||||
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 3.74 / Num. unique all: 1976 / % possible all: 93.2 | ||||||||||||||||||||||||
Reflection | *PLUS Num. obs: 41963 / Num. measured all: 146987 | ||||||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 93.2 % / Num. unique obs: 1976 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→20 Å / σ(F): 0
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Displacement parameters | Biso mean: 0.943 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→20 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.2121 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.7 Å2 | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / Rfactor Rfree: 0.3748 / Num. reflection obs: 3815 / Rfactor obs: 0.3516 |