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Yorodumi- PDB-6ddh: Crystal structure of the double mutant (D52N/R367Q) of NT5C2-537X... -
+Open data
-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 | |||||||||||||||
Components | Cytosolic purine 5'-nucleotidase | |||||||||||||||
Keywords | HYDROLASE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG | |||||||||||||||
Function / homology | Function and homology information 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 / IMP metabolic process / Ribavirin ADME / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||||||||
Authors | 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 | United States, 4items
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Citation | Journal: Cancer Cell / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ddh.cif.gz | 213.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ddh.ent.gz | 166.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ddh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/6ddh ftp://data.pdbj.org/pub/pdb/validation_reports/dd/6ddh | HTTPS FTP |
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-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 (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: NT5C2, NT5B, NT5CP, PNT5 / Plasmid: pLOC_NT5C2 / Cell (production host): Rosetta 2(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P49902, 5'-nucleotidase |
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#2: Chemical | ChemComp-IMP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |