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Open data
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Basic information
Entry | Database: PDB / ID: 2i5d | ||||||
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Title | Crystal Structure of Human Inosine Triphosphate Pyrophosphatase | ||||||
![]() | inosine triphosphate pyrophosphohydrolase | ||||||
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Function / homology | ![]() ITP catabolic process / deoxyribonucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Porta, J.C. / Kozmin, S.G. / Pavlov, Y.I. / Borgstahl, G.E.O. | ||||||
![]() | ![]() Title: Structure of the orthorhombic form of human inosine triphosphate pyrophosphatase. Authors: Porta, J. / Kolar, C. / Kozmin, S.G. / Pavlov, Y.I. / Borgstahl, G.E.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.8 KB | Display | ![]() |
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PDB format | ![]() | 42.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2carS S: Starting model for refinement |
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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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Details | The biological assembly is a monomer. |
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Components
#1: Protein | Mass: 21750.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9BY32, ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.96 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 27% PEG 3350 100mM HEPES pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 21, 2006 / Details: mirrors |
Radiation | Monochromator: Osmic VariMax Confocal Max-Flux Optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.63→105 Å / Num. all: 20838 / Num. obs: 20838 / % possible obs: 98.1 % / Redundancy: 5.9 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.048 / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 3.3 / Num. unique all: 20838 / Rsym value: 0.442 / % possible all: 98.2 |
-Phasing
Phasing MR | Rfactor: 0.493 / Cor.coef. Fo:Fc: 0.388
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 2CAR Resolution: 1.63→29.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.335 / SU ML: 0.082 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.124 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.782 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→29.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.67 Å / Total num. of bins used: 20
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