+Open data
-Basic information
Entry | Database: PDB / ID: 5hek | ||||||
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Title | crystal structure of M1.HpyAVI | ||||||
Components | Adenine specific DNA methyltransferase (DpnA) | ||||||
Keywords | DNA BINDING PROTEIN / M1.HpyAVI | ||||||
Function / homology | Function and homology information N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) activity / Transferases; Transferring one-carbon groups; Methyltransferases / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ma, B. / Zhang, H. / Liu, W. | ||||||
Citation | Journal: Oncotarget / Year: 2016 Title: Biochemical and structural characterization of a DNA N6-adenine methyltransferase from Helicobacter pylori Authors: Ma, B. / Ma, J. / Liu, D. / Guo, L. / Chen, H. / Ding, J. / Liu, W. / Zhang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hek.cif.gz | 314.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hek.ent.gz | 258.2 KB | Display | PDB format |
PDBx/mmJSON format | 5hek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/5hek ftp://data.pdbj.org/pub/pdb/validation_reports/he/5hek | HTTPS FTP |
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-Related structure data
Related structure data | 5hfjC 1g60S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 28211.697 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Strain: ATCC 700392 / 26695 / Gene: HP_0050 / Production host: Escherichia coli (E. coli) / References: UniProt: O24891 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / Details: 1.4 M ammonium tartrate / PH range: 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.093 Å / Num. obs: 27750 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.073 / Rsym value: 0.065 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 3.01→3.09 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.4 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G60 Resolution: 3→49.093 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→49.093 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -18.0304 Å / Origin y: 17.0395 Å / Origin z: -33.3439 Å
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Refinement TLS group | Selection details: all |