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Yorodumi- PDB-6bux: CRYSTAL STRUCTURE OF APOBEC3G CATALYTIC DOMAIN COMPLEX WITH SUBST... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bux | ||||||
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Title | CRYSTAL STRUCTURE OF APOBEC3G CATALYTIC DOMAIN COMPLEX WITH SUBSTRATE SSDNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / HYDROLASE / ANTIVIRAL DEFENCE / DNA CYTIDINE DEAMINASE / HYDROLASE-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 / negative regulation of viral process ...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 / negative regulation of viral process / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.856 Å | ||||||
Authors | Maiti, A. / Matsuo, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA. Authors: Maiti, A. / Myint, W. / Kanai, T. / Delviks-Frankenberry, K. / Sierra Rodriguez, C. / Pathak, V.K. / Schiffer, C.A. / Matsuo, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bux.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bux.ent.gz | 43.1 KB | Display | PDB format |
PDBx/mmJSON format | 6bux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bux_validation.pdf.gz | 432.7 KB | Display | wwPDB validaton report |
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Full document | 6bux_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | 6bux_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 6bux_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/6bux ftp://data.pdbj.org/pub/pdb/validation_reports/bu/6bux | HTTPS FTP |
-Related structure data
Related structure data | 3ir2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23062.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HC16*PLUS |
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#2: DNA chain | Mass: 2692.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20% PEG6000, 50 mM di-Sodium L-Malate; pH5.0, 30 mM CaCl2, Vapor Diffusion, Sitting Drop, Temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Oct 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.856→50 Å / Num. obs: 18860 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.989 / Rsym value: 0.083 / Net I/σ(I): 24.16 |
Reflection shell | Resolution: 1.856→1.93 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 6.3 / Num. unique obs: 1861 / CC1/2: 0.957 / Rsym value: 0.328 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IR2 (Chain A) Resolution: 1.856→38.608 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.856→38.608 Å
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Refine LS restraints |
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LS refinement shell |
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