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Yorodumi- PDB-6wma: Crystal structure of a soluble variant of full-length human APOBE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wma | ||||||
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Title | Crystal structure of a soluble variant of full-length human APOBEC3G (pH 7.6) | ||||||
Components |
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Keywords | HYDROLASE/DNA / APOBEC3G / ANTIVIRAL DEFENSE / HYDROLASE / DNA CYTIDINE DEAMINASE / HYDROLASE-DNA complex | ||||||
Function / homology | DNA Function and homology information | ||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Maiti, A. / Matsuo, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: Crystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains. Authors: Maiti, A. / Myint, W. / Delviks-Frankenberry, K.A. / Hou, S. / Kanai, T. / Balachandran, V. / Sierra Rodriguez, C. / Tripathi, R. / Kurt Yilmaz, N. / Pathak, V.K. / Schiffer, C.A. / Matsuo, H. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wma.cif.gz | 95 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wma.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 6wma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wma_validation.pdf.gz | 444.2 KB | Display | wwPDB validaton report |
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Full document | 6wma_full_validation.pdf.gz | 447.3 KB | Display | |
Data in XML | 6wma_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6wma_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/6wma ftp://data.pdbj.org/pub/pdb/validation_reports/wm/6wma | HTTPS FTP |
-Related structure data
Related structure data | 6wmbC 6wmcC 5k81S 6buxS 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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Unit cell |
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-Components
-Protein / DNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 42467.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3G / Production host: Escherichia coli (E. coli) |
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#2: DNA chain | Mass: 533.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 4 types, 153 molecules
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 2.85 Å3/Da / Density % sol: 56.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 0.03 M Citric acid, 0.07 M BIS-TRIS propane (pH 7.6) and 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→31.72 Å / Num. obs: 14930 / % possible obs: 90.1 % / Redundancy: 3 % / Biso Wilson estimate: 30.41 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1301 / CC1/2: 0.769 / % possible all: 80.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BUX CHAIN A AND 5K81 CHAIN A Resolution: 2.5→31.717 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.37 / 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 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.44 Å2 / Biso mean: 37.4646 Å2 / Biso min: 12.5 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→31.717 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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