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Yorodumi- PDB-8cxu: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cxu | ||||||
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Title | CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Compound 2 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / DNA Adenine Methylation / PROTEIN-DNA COMPLEX / TRANSFERASE / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA modification / methylation / nucleic acid binding Similarity search - Function | ||||||
Biological species | Clostridioides difficile 630 (bacteria) Clostridioides difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.28 Å | ||||||
Authors | Horton, J.R. / Zhou, J. / Cheng, X. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cxu.cif.gz | 934.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cxu.ent.gz | 631.4 KB | Display | PDB format |
PDBx/mmJSON format | 8cxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cxu_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8cxu_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8cxu_validation.xml.gz | 62.8 KB | Display | |
Data in CIF | 8cxu_validation.cif.gz | 89 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/8cxu ftp://data.pdbj.org/pub/pdb/validation_reports/cx/8cxu | HTTPS FTP |
-Related structure data
Related structure data | 8cxsC 8cxtC 8cxvC 8cxwC 8cxxC 8cxyC 8cxzC 8cy0C 8cy1C 8cy2C 8cy3C 8cy4C 8cy5C 7lnjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Clostridioides difficile 630 (bacteria) Strain: 630 / Gene: CD630_27580 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 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.) Clostridioides difficile (bacteria) #3: DNA chain | Mass: 4325.825 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria) |
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-Non-polymers , 4 types, 608 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-K / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.24 Å3/Da / Density % sol: 62.08 % |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→44.86 Å / Num. obs: 129038 / % possible obs: 93.5 % / Redundancy: 8.9 % / Biso Wilson estimate: 38.36 Å2 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.072 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.28→2.37 Å / Rmerge(I) obs: 1.7 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 10190 / CC1/2: 0.41 / CC star: 0.762 / Rpim(I) all: 0.733 / % possible all: 74.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 7LNJ Resolution: 2.28→44.86 Å / SU ML: 0.3167 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.193 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 47.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→44.86 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: -0.733466371478 Å / Origin y: 4.12094265208 Å / Origin z: -19.9618371531 Å
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Refinement TLS group | Selection details: all |