+Open data
-Basic information
Entry | Database: PDB / ID: 5zvb | ||||||
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Title | APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dT9) | ||||||
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 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 | 5zvb.cif.gz | 185.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zvb.ent.gz | 152.2 KB | Display | PDB format |
PDBx/mmJSON format | 5zvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/5zvb ftp://data.pdbj.org/pub/pdb/validation_reports/zv/5zvb | 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: 25154.236 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) 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: 2704.809 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: 2.5 Å3/Da / Density % sol: 50.75 % |
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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: Jun 6, 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: 1.98→50.01 Å / Num. obs: 37457 / % possible obs: 99.4 % / Redundancy: 14.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.146 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.98→2.02 Å / Rmerge(I) obs: 0.662 / CC1/2: 0.936 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→50.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 8.483 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.354 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.58 Å2 / Biso mean: 48.089 Å2 / Biso min: 24.61 Å2
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Refinement step | Cycle: final / Resolution: 2→50.01 Å
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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