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Yorodumi- PDB-1m0e: ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m0e | ||||||
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Title | ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASE | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Protein-DNA covalent complex / Mechanism based DNA methylation inhibitors / Zebularine / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system / methylation / DNA binding Similarity search - Function | ||||||
Biological species | Haemophilus haemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zhou, L. / Cheng, X. / Connolly, B.A. / Dickman, M.J. / Hurd, P.J. / Hornby, D.P. | ||||||
Citation | Journal: J.MOL.BIOL. / Year: 2002 Title: ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASES Authors: Zhou, L. / Cheng, X. / Connolly, B.A. / Dickman, M.J. / Hurd, P.J. / Hornby, D.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m0e.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m0e.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 1m0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m0e_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 1m0e_full_validation.pdf.gz | 465.8 KB | Display | |
Data in XML | 1m0e_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 1m0e_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/1m0e ftp://data.pdbj.org/pub/pdb/validation_reports/m0/1m0e | HTTPS FTP |
-Related structure data
Related structure data | 9mhtS S: Starting model for refinement |
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Similar structure data |
-Links
-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: DNA chain | Mass: 3623.368 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3688.401 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 37042.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P05102, EC: 2.1.1.73 |
#4: Chemical | ChemComp-SAH / |
#5: 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: 3.15 Å3/Da / Density % sol: 60.91 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, Ca acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 1999 Details: a parabolic collimating mirror placed upstream of monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→39.7 Å / Num. obs: 19591 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.5→2.61 Å / % possible all: 96.3 |
Reflection | *PLUS Highest resolution: 2.5 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 9MHT Resolution: 2.5→39.7 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 31.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 39.7 Å / Luzzati sigma a obs: 0.26 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→39.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.177 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.329 / Rfactor Rwork: 0.268 |