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Yorodumi- PDB-1q92: Crystal structure of human mitochondrial deoxyribonucleotidase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q92 | ||||||
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Title | Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor PMcP-U | ||||||
Components | 5(3)-deoxyribonucleotidase | ||||||
Keywords | HYDROLASE / alpha-beta rossman fold | ||||||
Function / homology | Function and homology information pyrimidine deoxyribonucleotide catabolic process / nucleotidase activity / dUMP catabolic process / Pyrimidine catabolism / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 5'-nucleotidase activity / DNA replication / mitochondrial matrix / nucleotide binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Rinaldo-Matthis, A. / Rampazzo, C. / Balzarini, J. / Reichard, P. / Bianchi, V. / Nordlund, P. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2004 Title: Crystal structures of the mitochondrial deoxyribonucleotidase in complex with two specific inhibitors Authors: Rinaldo-Matthis, A. / Rampazzo, C. / Balzarini, J. / Reichard, P. / Bianchi, V. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q92.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q92.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 1q92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/1q92 ftp://data.pdbj.org/pub/pdb/validation_reports/q9/1q92 | HTTPS FTP |
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-Related structure data
Related structure data | 1q91C 1mh9S 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: 22841.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NPB1, 5'-nucleotidase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-DRM / {[( |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.63 Å3/Da / Density % sol: 52.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: PEG 8000, potassium phosphate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 209551 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.4→1.45 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1MH9 Resolution: 1.4→25.32 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.982 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.719 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→25.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.402→1.439 Å / Total num. of bins used: 20 /
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