+Open data
-Basic information
Entry | Database: PDB / ID: 5k82 | ||||||
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Title | Crystal Structure of a Primate APOBEC3G N-Terminal Domain | ||||||
Components | Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G | ||||||
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 deaminase activity / retrotransposon silencing / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Macaca mulatta (Rhesus monkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.913 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 | 5k82.cif.gz | 167.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k82.ent.gz | 133 KB | Display | PDB format |
PDBx/mmJSON format | 5k82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/5k82 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/5k82 | HTTPS FTP |
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-Related structure data
Related structure data | 5k81SC 5k83C 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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Unit cell |
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-Components
#1: Protein | Mass: 23092.783 Da / Num. of mol.: 4 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: pGEX6P-1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: M1GSK9 #2: Chemical | ChemComp-ZN / |
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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: 5.79 Å3/Da / Density % sol: 78.76 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.9 M AmSO4, 0.1M Tris pH 8.0, 0.5 M NDSB-195 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99997 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→42.295 Å / Num. obs: 44596 / % possible obs: 98.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 1.9 / % possible all: 85.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K81 Resolution: 2.913→42.295 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 33.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.913→42.295 Å
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Refine LS restraints |
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LS refinement shell |
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