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Yorodumi- PDB-6nfk: Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nfk | ||||||
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Title | Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with loop 7 from APOBEC3G bound to iodide | ||||||
Components | DNA dC->dU-editing enzyme APOBEC-3B | ||||||
Keywords | HYDROLASE / APOBEC / deaminase | ||||||
Function / homology | Function and homology information mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / retrotransposon silencing / P-body / defense response to virus / innate immune response / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Shi, K. / Orellana, K. / Aihara, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Faseb Bioadv / Year: 2020 Title: Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B Authors: Shi, K. / Demir, O. / Carpenter, M.A. / Banerjee, S. / Harki, D.A. / Amaro, R.E. / Harris, R.S. / Aihara, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nfk.cif.gz | 126.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nfk.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 6nfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nfk_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 6nfk_full_validation.pdf.gz | 445.5 KB | Display | |
Data in XML | 6nfk_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 6nfk_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/6nfk ftp://data.pdbj.org/pub/pdb/validation_reports/nf/6nfk | HTTPS FTP |
-Related structure data
Related structure data | 6nflC 6nfmC 5cqdS S: Starting model for refinement C: citing same article (ref.) |
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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: 22843.818 Da / Num. of mol.: 1 Mutation: F200S, W228S, L230K, A242S, Y250S, E255Q, F308K, Y315D, D316Q, P317G, L318R, Y319C, K320Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3B / Production host: Escherichia coli (E. coli) References: UniProt: Q9UH17, single-stranded DNA cytosine deaminase | ||||
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#2: Chemical | #3: Chemical | ChemComp-IOD / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium Iodide, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→35.8 Å / Num. obs: 17023 / % possible obs: 99.37 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.024 / Rrim(I) all: 0.062 / Rsym value: 0.057 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.86→1.92 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1631 / CC1/2: 0.54 / Rpim(I) all: 0.54 / Rrim(I) all: 1.41 / Rsym value: 1.3 / % possible all: 98.43 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CQD Resolution: 1.86→35.78 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.02 / 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: 1.86→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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