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- PDB-6de0: Crystal structure of the single mutant (D52N) of NT5C2-Q523X in t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6de0 | |||||||||||||||
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Title | Crystal structure of the single mutant (D52N) of NT5C2-Q523X in the active state | |||||||||||||||
![]() | Cytosolic purine 5'-nucleotidase | |||||||||||||||
![]() | HYDROLASE | |||||||||||||||
Function / homology | ![]() nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity ...nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / Ribavirin ADME / IMP metabolic process / IMP catabolic process / Purine catabolism / allantoin metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Forouhar, F. / Dieck, C.L. / Tzoneva, G. / Carpenter, Z. / Ambesi-Impiombato, A. / Sanchez-Martin, M. / Kirschner-Schwabe, R. / Lew, S. / Seetharaman, J. / Ferrando, A.A. / Tong, L. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia. Authors: Dieck, C.L. / Tzoneva, G. / Forouhar, F. / Carpenter, Z. / Ambesi-Impiombato, A. / Sanchez-Martin, M. / Kirschner-Schwabe, R. / Lew, S. / Seetharaman, J. / Tong, L. / Ferrando, A.A. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.5 KB | Display | ![]() |
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PDB format | ![]() | 173.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.3 KB | Display | ![]() |
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Full document | ![]() | 440.6 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 31.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dd3C ![]() 6ddbC ![]() 6ddcC ![]() 6ddhC ![]() 6ddkC ![]() 6ddlC ![]() 6ddoC ![]() 6ddqC ![]() 6ddxC ![]() 6ddySC ![]() 6ddzC ![]() 6de1C ![]() 6de2C ![]() 6de3C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 62505.035 Da / Num. of mol.: 1 / Fragment: residues 1-523 / Mutation: D52N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7 / Details: 2M ammonium sulfate and 5% (v/v) 2-proponal |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX325HE / Detector: CCD / Date: May 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→48.939 Å / Num. obs: 47644 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 33.34 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.027 / Rrim(I) all: 0.072 / Χ2: 1.297 / Net I/av σ(I): 36.6 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 2371 / CC1/2: 0.94 / Rpim(I) all: 0.17 / Rrim(I) all: 0.46 / Χ2: 0.77 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6DDY Resolution: 2.05→48.939 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→48.939 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.2176 Å / Origin y: 38.9523 Å / Origin z: 19.4536 Å
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Refinement TLS group | Selection details: all |