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- PDB-6nfm: Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nfm | ||||||
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Title | Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with loop 7 from APOBEC3G | ||||||
![]() | DNA dC->dU-editing enzyme APOBEC-3B | ||||||
![]() | HYDROLASE / APOBEC / deaminase | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shi, K. / Aihara, H. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.1 KB | Display | ![]() |
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PDB format | ![]() | 35.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.3 KB | Display | ![]() |
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Full document | ![]() | 423.3 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nfkC ![]() 6nflC ![]() 5cqdS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 22844.803 Da / Num. of mol.: 1 Mutation: F200S, W228S, L230K, Y250S, F308K, Y315D, D316Q, P317G, L318R, Y319C, K320Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UH17, single-stranded DNA cytosine deaminase |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: LiCl, HEPES,PEG3350 |
-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: Feb 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→41.8 Å / Num. obs: 6968 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.07 / Rrim(I) all: 0.19 / Rsym value: 0.18 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.53→2.62 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.9 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 674 / CC1/2: 0.5 / Rpim(I) all: 0.7 / Rrim(I) all: 1.9 / Rsym value: 1.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CQD Resolution: 2.53→41.766 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.53→41.766 Å
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Refine LS restraints |
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LS refinement shell |
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