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Open data
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Basic information
Entry | Database: PDB / ID: 8j5e | ||||||
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Title | Crystal structure of kinase AbmG in complex with 4'-thiocytidine | ||||||
![]() | Deoxyadenosine/deoxycytidine kinase | ||||||
![]() | TRANSFERASE / Albomycin / biosynthesis | ||||||
Function / homology | deoxynucleoside kinase activity / Deoxynucleoside kinase domain / Deoxynucleoside kinase / phosphorylation / P-loop containing nucleoside triphosphate hydrolase / : / Deoxyadenosine/deoxycytidine kinase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ushimaru, R. / Mori, T. / Liu, H.-w. / Abe, I. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of kinase AbmG in complex with 4'-thiocytidine Authors: Ushimaru, R. / Mori, T. / Liu, H.-w. / Abe, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.6 KB | Display | ![]() |
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PDB format | ![]() | 47.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 752.4 KB | Display | ![]() |
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Full document | ![]() | 753.6 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Unit cell |
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Components
#1: Protein | Mass: 27404.893 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Author's provided sample sequence corresponds to the reference sequence (A0A370RDE4) in the UniProt database. Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#2: Chemical | ChemComp-TQR / Mass: 259.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O4S / Feature type: SUBJECT OF INVESTIGATION |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium nitrate, 28% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44.47 Å / Num. obs: 25964 / % possible obs: 99.9 % / Redundancy: 14.9 % / Biso Wilson estimate: 16.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1332 / CC1/2: 0.871 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 20.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→44.47 Å
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Refine LS restraints |
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LS refinement shell |
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