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Yorodumi- PDB-8e5e: Crystal structure of double-stranded DNA deaminase toxin DddA in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8e5e | |||||||||
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Title | Crystal structure of double-stranded DNA deaminase toxin DddA in complex with DNA with the target cytosine flipped into the active site | |||||||||
Components |
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Keywords | TOXIN/DNA / toxin / DNA binding / deaminase / TOXIN-DNA complex | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / toxin activity / hydrolase activity / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Burkholderia cenocepacia (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | |||||||||
Authors | Yin, L.L. / Shi, K. / Aihara, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2023 Title: Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA. Authors: Yin, L. / Shi, K. / Aihara, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e5e.cif.gz | 101 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e5e.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 8e5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e5e_validation.pdf.gz | 429.5 KB | Display | wwPDB validaton report |
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Full document | 8e5e_full_validation.pdf.gz | 430.6 KB | Display | |
Data in XML | 8e5e_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 8e5e_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/8e5e ftp://data.pdbj.org/pub/pdb/validation_reports/e5/8e5e | HTTPS FTP |
-Related structure data
Related structure data | 8e5dC 6u08S 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14686.213 Da / Num. of mol.: 1 / Mutation: E1347A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Gene: dddA / Production host: Escherichia coli (E. coli) References: UniProt: P0DUH5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines |
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-DNA chain , 2 types, 2 molecules CB
#2: DNA chain | Mass: 4296.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 4265.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 4 molecules
#4: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 2.55 Å3/Da / Density % sol: 51.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 25 % polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→44.87 Å / Num. obs: 8887 / % possible obs: 98 % / Redundancy: 5.7 % / CC1/2: 0.979 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.079 / Rrim(I) all: 0.171 / Χ2: 2.41 / Net I/σ(I): 45.6 / Num. measured all: 50693 |
Reflection shell | Resolution: 2.62→2.74 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 1.762 / Num. measured all: 7585 / Num. unique obs: 1076 / CC1/2: 0.589 / Rpim(I) all: 0.706 / Rrim(I) all: 1.904 / Χ2: 1.18 / Net I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6U08 Resolution: 2.62→35.78 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.21 / 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: 2.62→35.78 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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