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- PDB-8pqs: Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis therm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pqs | ||||||
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Title | Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 E88A Mutant | ||||||
![]() | Nucleoside 2-deoxyribosyltransferase | ||||||
![]() | TRANSFERASE / Mutant | ||||||
Function / homology | deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / transferase activity / 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 | ![]() | 140.8 KB | Display | ![]() |
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PDB format | ![]() | 110.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.5 KB | Display | ![]() |
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Full document | ![]() | 444.3 KB | Display | |
Data in XML | ![]() | 26.9 KB | Display | |
Data in CIF | ![]() | 39 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pqpC ![]() 8pqqC ![]() 8pqrC ![]() 8pqtC ![]() 8qc0C ![]() 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: 17762.307 Da / Num. of mol.: 4 / Mutation: E88A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7203 / Gene: Chro_1188 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.03 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 21.43% PEG 6000; 0.1 M Tris; 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: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→70.21 Å / Num. obs: 73355 / % possible obs: 99.96 % / Redundancy: 38.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.294 / Rrim(I) all: 0.0298 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.89→1.92 Å / Redundancy: 34.7 % / Rmerge(I) obs: 5.938 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 3617 / CC1/2: 0.343 / Rrim(I) all: 6.026 / % possible all: 98.61 |
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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: 1.95→44.4 Å
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Refine LS restraints |
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LS refinement shell |
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