+Open data
-Basic information
Entry | Database: PDB / ID: 1boo | ||||||
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Title | PVUII DNA METHYLTRANSFERASE (CYTOSINE-N4-SPECIFIC) | ||||||
Components | PROTEIN (N-4 CYTOSINE-SPECIFIC METHYLTRANSFERASE PVU II) | ||||||
Keywords | TRANSFERASE / TYPE II DNA-(CYTOSINE N4) METHYLTRANSFERASE / AMINO METHYLATION / SELENOMETHIONINE / MULTIWAVELENGTH ANOMALOUS DIFFRACTION | ||||||
Function / homology | Function and homology information site-specific DNA-methyltransferase (cytosine-N4-specific) / : / site-specific DNA-methyltransferase (cytosine-N4-specific) activity / : / N-methyltransferase activity / DNA restriction-modification system / DNA binding Similarity search - Function | ||||||
Biological species | Proteus vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Gong, W. / O'Gara, M. / Blumenthal, R.M. / Cheng, X. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 1997 Title: Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Authors: Gong, W. / O'Gara, M. / Blumenthal, R.M. / Cheng, X. #1: Journal: Eur.J.Biochem. / Year: 1997 Title: Expression, Purification, Mass Spectrometry, Crystallization and Multiwavelength Anomalous Diffraction of Selenomethionyl PvuII DNA Methyltransferase (Cytosine-N4-Specific) Authors: O'Gara, M. / Adams, G.M. / Gong, W. / Kobayashi, R. / Blumenthal, R.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 | 1boo.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1boo.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 1boo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/1boo ftp://data.pdbj.org/pub/pdb/validation_reports/bo/1boo | HTTPS FTP |
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-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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.6975, -0.6041, 0.3855), Vector: |
-Components
#1: Protein | Mass: 36956.207 Da / Num. of mol.: 1 Fragment: STARTING FROM THE INTERNAL TRANSLATION INITIATOR AT MET14 Mutation: N TERMIANL DELETION (RESIDUES 1-13) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus vulgaris (bacteria) / Species (production host): Escherichia coli Production host: Escherichia coli str. K-12 substr. DH10B (bacteria) Strain (production host): DH10B References: UniProt: P11409, site-specific DNA-methyltransferase (cytosine-N4-specific) |
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#2: Chemical | ChemComp-SAH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 38.2 % | ||||||||||||||||||||
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Crystal grow | pH: 7.2 Details: 0.1 M HEPES PH 7.2, 0.2 M SODIUM ACETATE 20% POLYETHYLENE GLYCOL 400 | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98233,0.98211,0.92,1.072 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→30 Å / Num. obs: 14886 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.68 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.5 | |||||||||||||||
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 5.5 / % possible all: 97.5 | |||||||||||||||
Reflection | *PLUS Num. measured all: 54787 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 97.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→30 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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