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Yorodumi- PDB-6mht: TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND DNA C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mht | |||||||||
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Title | TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND DNA CONTAINING 4'-THIO-2'DEOXYCYTIDINE 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 / methylation / DNA binding Similarity search - Function | |||||||||
Biological species | Haemophilus haemolyticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.05 Å | |||||||||
Authors | Cheng, X. | |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 1997 Title: DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase. Authors: Kumar, S. / Horton, J.R. / Jones, G.D. / Walker, R.T. / Roberts, R.J. / Cheng, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mht.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mht.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 6mht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mht_validation.pdf.gz | 452.3 KB | Display | wwPDB validaton report |
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Full document | 6mht_full_validation.pdf.gz | 471.1 KB | Display | |
Data in XML | 6mht_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 6mht_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/6mht ftp://data.pdbj.org/pub/pdb/validation_reports/mh/6mht | HTTPS FTP |
-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: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: DNA chain | Mass: 3733.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Protein | Mass: 37042.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / References: UniProt: P05102, EC: 2.1.1.73 |
#4: Chemical | ChemComp-SAM / |
#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: 65.02 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 5.6 Details: 1.4-1.8 M AMMONIUM SULFATE 50 MM CITRATE PH 5.6, temperature 293.0K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 16 ℃ / Method: unknown / Details: O'Gara, M., (1996) J. Mol. Biol., 261, 634. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. obs: 32880 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.33 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.1 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 5MHT Resolution: 2.05→5 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.05→5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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