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Open data
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Basic information
Entry | Database: PDB / ID: 5zva | ||||||
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Title | APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dC9) | ||||||
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Function / homology | ![]() apolipoprotein B mRNA editing enzyme complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() DNA-binding vector pODB80 (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cheng, C. / Zhang, T.L. / Wang, C.X. / Lan, W.X. / Ding, J.P. / Cao, C.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA Authors: Cheng, C. / Zhang, T. / Wang, C. / Lan, W. / Ding, J. / Cao, C. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.3 KB | Display | ![]() |
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PDB format | ![]() | 148.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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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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Unit cell |
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Components
#1: Protein | Mass: 24919.762 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: All residures includes purification tag of A3F(6His+thrombin cleavage tag+ chimeric A3F) (reference: K. Siu, et al. Nat. Commun. 2013, 4, 2593. PDB code:4J4J),All residures includes ...Details: All residures includes purification tag of A3F(6His+thrombin cleavage tag+ chimeric A3F) (reference: K. Siu, et al. Nat. Commun. 2013, 4, 2593. PDB code:4J4J),All residures includes purification tag of A3F(6His+thrombin cleavage tag+ chimeric A3F)(reference: K. Siu, et al. Nat. Commun. 2013, 4, 2593. PDB code:4J4J) Source: (gene. exp.) ![]() ![]() Production host: prokaryotic environmental samples (environmental samples) References: UniProt: Q9HC16, UniProt: Q8IUX4, ![]() #2: DNA chain | | Mass: 2993.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) DNA-binding vector pODB80 (others) #3: Chemical | #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 53.92 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05M sodium cacodylate, pH 6.5, and 30%(v/v) 2-methyl-2,4-pentanediol(MPD) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jul 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→45.68 Å / Num. obs: 23245 / % possible obs: 98.5 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.619 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Displacement parameters | Biso mean: 50.96 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→45.68 Å
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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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