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- PDB-6ddh: Crystal structure of the double mutant (D52N/R367Q) of NT5C2-537X... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ddh | |||||||||||||||
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Title | Crystal structure of the double mutant (D52N/R367Q) of NT5C2-537X in the active state, Northeast Structural Genomics Target | |||||||||||||||
![]() | Cytosolic purine 5'-nucleotidase | |||||||||||||||
![]() | HYDROLASE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG | |||||||||||||||
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. ...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. / Northeast Structural Genomics Consortium (NESG) | |||||||||||||||
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 | ![]() | 213.9 KB | Display | ![]() |
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PDB format | ![]() | 166.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 744.1 KB | Display | ![]() |
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Full document | ![]() | 746.1 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dd3C ![]() 6ddbC ![]() 6ddcC ![]() 6ddkC ![]() 6ddlC ![]() 6ddoC ![]() 6ddqC ![]() 6ddxC ![]() 6ddyC ![]() 6ddzC ![]() 6de0C ![]() 6de1C ![]() 6de2C ![]() 6de3C ![]() 2xcwS 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
#1: Protein | Mass: 63927.688 Da / Num. of mol.: 1 / Fragment: residues 1-536 / Mutation: D52N, R367Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-IMP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7.5 Details: 0.1 M HEPES (pH 7.5), 20% (w/v) PEG 1000, and 0.1 M ammonium nitrate, 5 mM ATP, 5 mM IMP, 5 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→48.661 Å / Num. obs: 32593 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 37.7 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Rrim(I) all: 0.1 / Χ2: 1.01 / Net I/av σ(I): 28 / Net I/σ(I): 28 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4 / Num. unique obs: 1622 / CC1/2: 0.98 / Rpim(I) all: 0.2 / Rrim(I) all: 0.52 / Χ2: 0.83 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2XCW Resolution: 2.35→48.661 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→48.661 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: -0.3093 Å / Origin y: 25.0343 Å / Origin z: 45.859 Å
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Refinement TLS group | Selection details: all |