+Open data
-Basic information
Entry | Database: PDB / ID: 5lod | ||||||
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Title | Crystal structure of HhaI DNA methyltransferase in APO form | ||||||
Components | Modification methylase HhaI | ||||||
Keywords | TRANSFERASE / M.HhaI / C5-METHYLCYTOSINE / APO FORM / DNA methyltransferase | ||||||
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 parahaemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Rondelet, G. / Wouters, J. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Future Med Chem / Year: 2017 Title: Inhibition studies of DNA methyltransferases by maleimide derivatives of RG108 as non-nucleoside inhibitors. Authors: Rondelet, G. / Fleury, L. / Faux, C. / Masson, V. / Dubois, J. / Arimondo, P.B. / Willems, L. / Wouters, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lod.cif.gz | 141.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lod.ent.gz | 112.2 KB | Display | PDB format |
PDBx/mmJSON format | 5lod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lod_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 5lod_full_validation.pdf.gz | 445.4 KB | Display | |
Data in XML | 5lod_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 5lod_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/5lod ftp://data.pdbj.org/pub/pdb/validation_reports/lo/5lod | HTTPS FTP |
-Related structure data
Related structure data | 2hmyS 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: Protein | Mass: 37042.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus parahaemolyticus (bacteria) Gene: hhaIM / Production host: Escherichia coli (E. coli) References: UniProt: P05102, DNA (cytosine-5-)-methyltransferase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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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: 2.16 Å3/Da / Density % sol: 42.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: AMMONIUM SULFATE 50 mM, CITRATE 100mM, 32% (w/v) PEG-4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Type: OTHER / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.73 Å / Num. obs: 49539 / % possible obs: 99.61 % / Redundancy: 3.68 % / CC1/2: 0.98 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.42 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.77 / CC1/2: 0.907 / % possible all: 99.74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HMY Resolution: 1.9→41.728 Å / FOM work R set: 0.8508 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.36 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.53 Å2 / Biso mean: 34.54 Å2 / Biso min: 16.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→41.728 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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