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Yorodumi- PDB-10mh: TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND HEMIM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 10mh | ||||||
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Title | TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND HEMIMETHYLATED DNA CONTAINING 5,6-DIHYDRO-5-AZACYTOSINE AT THE TARGET | ||||||
Components |
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Keywords | TRANSFERASE/DNA / TRANSFERASE / METHYLTRANSFERASE / RESTRICTION SYSTEM / COMPLEX (METHYLTRANSFERASE- DNA) / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system / DNA binding Similarity search - Function | ||||||
Biological species | Haemophilus haemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.55 Å | ||||||
Authors | Sheikhnejad, G. / Brank, A. / Christman, J.K. / Goddard, A. / Alvarez, E. / Ford Junior, H. / Marquez, V.E. / Marasco, C.J. / Sufrin, J.R. / O'Gara, M. / Cheng, X. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine. Authors: Sheikhnejad, G. / Brank, A. / Christman, J.K. / Goddard, A. / Alvarez, E. / Ford Jr., H. / Marquez, V.E. / Marasco, C.J. / Sufrin, J.R. / O'gara, M. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 10mh.cif.gz | 101 KB | Display | PDBx/mmCIF format |
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PDB format | pdb10mh.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 10mh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/0m/10mh ftp://data.pdbj.org/pub/pdb/validation_reports/0m/10mh | HTTPS FTP |
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-Related structure data
Related structure data | 5mhtS 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
#1: DNA chain | Mass: 3637.395 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3704.404 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: 3.52 Å3/Da / Density % sol: 65.03 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 10% (W/V) PEG 8000 50 MM CALCIUM ACETATE 50 MM SODIUM CACODYLATE PH 6.5 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 15976 / % possible obs: 77.2 % / Redundancy: 3.23 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 2.89 / % possible all: 50.2 |
Reflection | *PLUS Num. measured all: 51683 |
Reflection shell | *PLUS % possible obs: 50.2 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 5MHT Resolution: 2.55→29.3 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.55→29.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.67 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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