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- PDB-4b56: Structure of ectonucleotide pyrophosphatase-phosphodiesterase-1 (NPP1) -
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Open data
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Basic information
Entry | Database: PDB / ID: 4b56 | |||||||||
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Title | Structure of ectonucleotide pyrophosphatase-phosphodiesterase-1 (NPP1) | |||||||||
![]() | ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 1 | |||||||||
![]() | HYDROLASE | |||||||||
Function / homology | ![]() articular cartilage development / microglial cell migration / Vitamin B2 (riboflavin) metabolism / response to platelet-derived growth factor / ligamentous ossification / response to vitamin B6 / cellular response to sodium phosphate / GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity ...articular cartilage development / microglial cell migration / Vitamin B2 (riboflavin) metabolism / response to platelet-derived growth factor / ligamentous ossification / response to vitamin B6 / cellular response to sodium phosphate / GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / organic phosphonate metabolic process / post-embryonic forelimb morphogenesis / UTP diphosphatase activity / tooth mineralization / inorganic diphosphate transport / hematopoietic stem cell migration to bone marrow / leukocyte activation involved in inflammatory response / phosphodiesterase I / bone growth / biomineral tissue development / sensory perception of temperature stimulus / dinucleotide phosphatase activity / coenzyme A diphosphatase activity / basal dendrite / coenzyme A catabolic process / pyrophosphatase activity / vascular associated smooth muscle cell migration / nucleotide diphosphatase / nucleoside triphosphate catabolic process / inhibition of non-skeletal tissue mineralization / response to Gram-positive bacterium / magnesium ion homeostasis / diphosphate metabolic process / endochondral bone morphogenesis / bone trabecula formation / vitamin D3 metabolic process / cementum mineralization / central nervous system myelination / vascular associated smooth muscle cell proliferation / nucleoside triphosphate diphosphatase activity / bone mineralization involved in bone maturation / mucus secretion / response to sodium phosphate / ATP diphosphatase activity / phosphate ion homeostasis / negative regulation of bone mineralization / sensory perception of mechanical stimulus / plasma cell differentiation / B-1 B cell homeostasis / phosphodiesterase I activity / artery development / scavenger receptor activity / microglia differentiation / collagen-activated signaling pathway / cellular homeostasis / apoptotic process involved in development / endochondral ossification / apical dendrite / bone remodeling / phosphoric diester hydrolase activity / regulation of bone mineralization / hormone metabolic process / inflammatory response to antigenic stimulus / negative regulation of ossification / adult walking behavior / cartilage development / aorta development / middle ear morphogenesis / oligodendrocyte apoptotic process / odontogenesis / axon regeneration / fat pad development / skin development / smoothened signaling pathway / polysaccharide binding / response to ATP / muscle cell cellular homeostasis / spinal cord development / negative regulation of fat cell differentiation / bone mineralization / fat cell differentiation / defense response to protozoan / glucose import / phosphatase activity / response to dietary excess / response to magnesium ion / macrophage differentiation / T cell differentiation / : / 3',5'-cyclic-AMP phosphodiesterase activity / fibroblast growth factor receptor signaling pathway / calcium ion homeostasis / vasculogenesis / adipose tissue development / ATP metabolic process / bone resorption / mitochondrion organization / adult locomotory behavior / ossification / osteoclast differentiation Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Jansen, S. / Perrakis, A. / Ulens, C. / Winkler, C. / Andries, M. / Joosten, R.P. / Van Acker, M. / Luyten, F.P. / Moolenaar, W.H. / Bollen, M. | |||||||||
![]() | ![]() Title: Structure of Npp1, an Ectonucleotide Pyrophosphatase/Phosphodiesterase Involved in Tissue Calcification. Authors: Jansen, S. / Perrakis, A. / Ulens, C. / Winkler, C. / Andries, M. / Joosten, R.P. / Van Acker, M. / Luyten, F.P. / Moolenaar, W.H. / Bollen, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 656.4 KB | Display | ![]() |
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PDB format | ![]() | 549.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 55.5 KB | Display | |
Data in CIF | ![]() | 74.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xrgS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 169 - 902 / Label seq-ID: 83 - 816
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 94264.055 Da / Num. of mol.: 2 / Fragment: RESIDUES 87-906 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P06802, phosphodiesterase I, nucleotide diphosphatase |
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-Sugars , 4 types, 8 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 8 molecules ![](data/chem/img/ZN.gif)
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#5: Chemical | ChemComp-ZN / #6: Chemical | #7: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.3 % / Description: NONE |
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Crystal grow | pH: 8 Details: 100 NL PROTEIN SOLUTION WITH 100 NL 10% PROPANOL, 0.1 M IMIDAZOLE AT PH 8.0 AND 3% 1,4-DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 3→48.47 Å / Num. obs: 51597 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 110 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XRG Resolution: 3→48.47 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 38.967 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R: 4.29 / ESU R Free: 0.356 / 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 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 116.185 Å2
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Refinement step | Cycle: LAST / Resolution: 3→48.47 Å
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Refine LS restraints |
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