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- PDB-8e9a: Crystal structure of AsfvPolX in complex with 10-23 DNAzyme and Mg -
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Open data
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Basic information
Entry | Database: PDB / ID: 8e9a | ||||||
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Title | Crystal structure of AsfvPolX in complex with 10-23 DNAzyme and Mg | ||||||
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![]() | TRANSFERASE/DNA / DNAzyme / DNA / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() virion component / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cramer, E.R. / Robart, A.R. / Kaya, A.I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformation. Authors: Cramer, E.R. / Starcovic, S.A. / Avey, R.M. / Kaya, A.I. / Robart, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 236 KB | Display | ![]() |
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PDB format | ![]() | 184.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.5 KB | Display | ![]() |
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Full document | ![]() | 468.9 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xm8S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 20438.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 16102.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.76 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium chloride, 0.1 M HEPES (pH 7.5), and 25% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 11, 2021 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→139.85 Å / Num. obs: 21227 / % possible obs: 97.53 % / Redundancy: 3.4 % / Biso Wilson estimate: 74.42 Å2 / CC1/2: 0.977 / Net I/σ(I): 2.1 |
Reflection shell | Resolution: 2.69→2.82 Å / Num. unique obs: 2818 / CC1/2: 0.305 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XM8 Resolution: 2.69→69.92 Å / SU ML: 0.478 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.7597 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.69→69.92 Å
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Refine LS restraints |
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LS refinement shell |
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