+Open data
-Basic information
Entry | Database: PDB / ID: 5zva | ||||||
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Title | APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dC9) | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / APOBEC3F / HIV-1 / deamination / STRUCTURAL PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information apolipoprotein B mRNA editing enzyme complex / dCTP deaminase activity / cytidine deamination / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / : / cytidine deaminase activity / clearance of foreign intracellular DNA ...apolipoprotein B mRNA editing enzyme complex / dCTP deaminase activity / cytidine deamination / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / : / cytidine deaminase activity / clearance of foreign intracellular DNA / positive regulation of gene expression via chromosomal CpG island demethylation / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of viral process / : / retrotransposon silencing / negative regulation of viral genome replication / APOBEC3G mediated resistance to HIV-1 infection / positive regulation of defense response to virus by host / Vif-mediated degradation of APOBEC3G / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) DNA-binding vector pODB80 (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Cheng, C. / Zhang, T.L. / Wang, C.X. / Lan, W.X. / Ding, J.P. / Cao, C.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Chin.J.Chem. / Year: 2018 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zva.cif.gz | 179.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zva.ent.gz | 148.1 KB | Display | PDB format |
PDBx/mmJSON format | 5zva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/5zva ftp://data.pdbj.org/pub/pdb/validation_reports/zv/5zva | HTTPS FTP |
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-Related structure data
-Links
-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.) Homo sapiens (human) / Gene: APOBEC3G, MDS019, APOBEC3F Production host: prokaryotic environmental samples (environmental samples) References: UniProt: Q9HC16, UniProt: Q8IUX4, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
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: 0.9793 Å / Relative weight: 1 |
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: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→45.68 Å / SU B: 12.618 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.193 / Details: U VALUES : WITH TLS ADDED
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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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