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- PDB-8qc0: Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis therm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qc0 | ||||||
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Title | Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 WT ribosylated | ||||||
![]() | Nucleoside 2-deoxyribosyltransferase | ||||||
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Function / homology | deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / ![]() ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tang, P. / Harding, C.J. / Czekster, C.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase. Authors: Tang, P. / Harding, C.J. / Dickson, A.L. / da Silva, R.G. / Harrison, D.J. / Czekster, C.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.1 KB | Display | ![]() |
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PDB format | ![]() | 108.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8pqpC ![]() 8pqqC ![]() 8pqrC ![]() 8pqsC ![]() 8pqtC ![]() 8rh3C C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 17689.146 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7203 / Gene: Chro_1188 / Production host: ![]() ![]() ![]() #2: Sugar | ChemComp-RIB / ![]() #3: Chemical | ChemComp-ZN / #4: 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: 3.23 Å3/Da / Density % sol: 61.92 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 21.43% v/v PEG 6000; 0.1 M Tris pH 8; 0.5 M Zinc chloride |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.02→53.5 Å / Num. obs: 59536 / % possible obs: 100 % / Redundancy: 39.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.031 / Rrim(I) all: 0.194 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.02→2.05 Å / Redundancy: 42.1 % / Rmerge(I) obs: 5.534 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2939 / CC1/2: 0.286 / Rpim(I) all: 0.862 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→44.27 Å
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Refine LS restraints |
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LS refinement shell |
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