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Yorodumi- PDB-5k83: Crystal Structure of a Primate APOBEC3G N-Domain, in Complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k83 | ||||||
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Title | Crystal Structure of a Primate APOBEC3G N-Domain, in Complex with ssDNA | ||||||
Components |
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Keywords | HYDROLASE / APOBEC3G / Vif / HIV / APOBEC | ||||||
Function / homology | Function and homology information Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / retrotransposon silencing / P-body / defense response to virus ...Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / retrotransposon silencing / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Macaca mulatta (Rhesus monkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Xiao, X. / Li, S.-X. / Yang, H. / Chen, X.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2016 Title: Crystal structures of APOBEC3G N-domain alone and its complex with DNA. Authors: Xiao, X. / Li, S.X. / Yang, H. / Chen, X.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k83.cif.gz | 253.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k83.ent.gz | 202.7 KB | Display | PDB format |
PDBx/mmJSON format | 5k83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k83_validation.pdf.gz | 492.1 KB | Display | wwPDB validaton report |
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Full document | 5k83_full_validation.pdf.gz | 504.8 KB | Display | |
Data in XML | 5k83_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 5k83_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/5k83 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/5k83 | HTTPS FTP |
-Related structure data
Related structure data | 5k81SC 5k82C 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 23092.783 Da / Num. of mol.: 6 Fragment: UNP residues 1-195 (139CQKRDGPH146 replaced by AEAG) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: APOBEC3G / Plasmid: pGEX-6P-1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: M1GSK9 #2: DNA chain | Mass: 2996.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Macaca mulatta (Rhesus monkey) #3: Chemical | ChemComp-ZN / #4: 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: 2.9 Å3/Da / Density % sol: 57.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.0, 6% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→45.792 Å / Num. obs: 63261 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 26 |
Reflection shell | Resolution: 2.39→2.48 Å / Redundancy: 5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K81 Resolution: 2.39→45.792 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.32 Å2 / Biso mean: 45.3537 Å2 / Biso min: 14.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.39→45.792 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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