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- PDB-1z4m: Structure of the D41N variant of the human mitochondrial deoxyrib... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1z4m | ||||||
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Title | Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with uridine 5'-monophosphate | ||||||
![]() | 5'(3')-deoxyribonucleotidase | ||||||
![]() | HYDROLASE / alfa beta fold | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wallden, K. / Ruzzenente, B. / Rinaldo-Matthis, A. / Bianchi, V. / Nordlund, P. | ||||||
![]() | ![]() Title: Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase Authors: Wallden, K. / Ruzzenente, B. / Rinaldo-Matthis, A. / Bianchi, V. / Nordlund, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.7 KB | Display | ![]() |
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PDB format | ![]() | 42.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 986.9 KB | Display | ![]() |
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Full document | ![]() | 989.1 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1z4iC ![]() 1z4jC ![]() 1z4kC ![]() 1z4lC ![]() 1z4pC ![]() 1z4qC 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: 22840.135 Da / Num. of mol.: 1 / Mutation: D41N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NPB1, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-U5P / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % |
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Crystal grow | pH: 4.5 / Details: pH 4.5 |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Detector: CCD / Date: Jan 27, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 32144 / % possible obs: 98.5 % / Redundancy: 5 % / Rsym value: 0.047 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.334 / % possible all: 98.3 |
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Processing
Software | Name: REFMAC / Version: 5.2.0005 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.348 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Total num. of bins used: 20
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