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- PDB-8cxt: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cxt | ||||||
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Title | CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor N6-benzyladenosine (Compound 1) | ||||||
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![]() | DNA BINDING PROTEIN/DNA / DNA Adenine Methylation / PROTEIN-DNA COMPLEX / TRANSFERASE / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() macromolecule modification / N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / methylation / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Horton, J.R. / Zhou, J. / Cheng, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence. Authors: Zhou, J. / Horton, J.R. / Menna, M. / Fiorentino, F. / Ren, R. / Yu, D. / Hajian, T. / Vedadi, M. / Mazzoccanti, G. / Ciogli, A. / Weinhold, E. / Huben, M. / Blumenthal, R.M. / Zhang, X. / ...Authors: Zhou, J. / Horton, J.R. / Menna, M. / Fiorentino, F. / Ren, R. / Yu, D. / Hajian, T. / Vedadi, M. / Mazzoccanti, G. / Ciogli, A. / Weinhold, E. / Huben, M. / Blumenthal, R.M. / Zhang, X. / Mai, A. / Rotili, D. / Cheng, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 480.4 KB | Display | ![]() |
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PDB format | ![]() | 309.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 56.8 KB | Display | |
Data in CIF | ![]() | 77.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cxsC ![]() 8cxuC ![]() 8cxvC ![]() 8cxwC ![]() 8cxxC ![]() 8cxyC ![]() 8cxzC ![]() 8cy0C ![]() 8cy1C ![]() 8cy2C ![]() 8cy3C ![]() 8cy4C ![]() 8cy5C ![]() 7lnjS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 68887.172 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 630 / Gene: CD630_27580 / Production host: ![]() ![]() References: UniProt: Q183J3, site-specific DNA-methyltransferase (adenine-specific) |
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-DNA chain , 2 types, 6 molecules DFHEGI
#2: DNA chain | Mass: 4232.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() #3: DNA chain | Mass: 4325.825 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 4 types, 138 molecules ![](data/chem/img/K.gif)
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#4: Chemical | ChemComp-K / #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.74 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 21~24% (w/v) polyethylene glycol 3350, 0.1 M Tris-HCl pH 7.0~7.5, 0.28 M potassium citrate PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→44.23 Å / Num. obs: 91039 / % possible obs: 100 % / Redundancy: 23.8 % / Biso Wilson estimate: 63.41 Å2 / Rmerge(I) obs: 0.337 / Rpim(I) all: 0.063 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.61→2.74 Å / Rmerge(I) obs: 2.124 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8954 / CC1/2: 0.468 / CC star: 0.799 / Rpim(I) all: 0.678 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7LNJ Resolution: 2.61→44.23 Å / SU ML: 0.3975 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7442 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61→44.23 Å
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Refine LS restraints |
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LS refinement shell |
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