+Open data
-Basic information
Entry | Database: PDB / ID: 4gtz | |||||||||
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Title | Crystal structure of mouse Enpp1 in complex with CMP | |||||||||
Components | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I | |||||||||
Keywords | HYDROLASE / Bone Mineralization / Phosphodiesterase | |||||||||
Function / homology | Function and homology information dinucleotide phosphatase activity / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipase D / phosphatidylcholine catabolic process / positive regulation of lamellipodium morphogenesis / lysophospholipase activity / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity ...dinucleotide phosphatase activity / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipase D / phosphatidylcholine catabolic process / positive regulation of lamellipodium morphogenesis / lysophospholipase activity / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity / hydrolase activity, acting on ester bonds / polysaccharide binding / negative regulation of cell-matrix adhesion / positive regulation of oligodendrocyte differentiation / positive regulation of epithelial cell migration / positive regulation of focal adhesion assembly / estrous cycle / phospholipid metabolic process / positive regulation of substrate adhesion-dependent cell spreading / cell chemotaxis / positive regulation of peptidyl-tyrosine phosphorylation / nucleic acid binding / immune response / positive regulation of cell population proliferation / calcium ion binding / extracellular space / zinc ion binding / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.191 Å | |||||||||
Authors | Kato, K. / Nishimasu, H. / Ishitani, R. / Nureki, O. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling. Authors: Kato, K. / Nishimasu, H. / Okudaira, S. / Mihara, E. / Ishitani, R. / Takagi, J. / Aoki, J. / Nureki, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gtz.cif.gz | 572.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gtz.ent.gz | 470.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gtz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gtz_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4gtz_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4gtz_validation.xml.gz | 50 KB | Display | |
Data in CIF | 4gtz_validation.cif.gz | 67.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/4gtz ftp://data.pdbj.org/pub/pdb/validation_reports/gt/4gtz | HTTPS FTP |
-Related structure data
Related structure data | 4gtwSC 4gtxC 4gtyC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 94560.203 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 51-59, 92-905 / Mutation: K59R Source method: isolated from a genetically manipulated source Details: THE FUSION PROTEIN OF ENPP2 (UNP RESIDUES 51-59) AND ENPP1 (UNP RESIDUES 92-905) Source: (gene. exp.) Mus musculus (house mouse) / Gene: Enpp2, Npps2, Pdnp2, Enpp1, mCG_9001 / Plasmid: modified pcDNA3.1 / Cell (production host): mammalian cells / Cell line (production host): HEK293S GnT1- / Production host: Homo sapiens (human) References: UniProt: Q9R1E6, UniProt: G3X9S2, alkylglycerophosphoethanolamine phosphodiesterase |
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-Sugars , 3 types, 6 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 |
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#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: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 8 molecules
#5: Chemical | #6: Chemical | ChemComp-ZN / #7: Chemical | |
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-Details
Sequence details | THE FUSION PROTEIN OF ENPP2 (UNP RESIDUES 51-59) AND ENPP1 (UNP RESIDUES 92-905) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.32 % / Mosaicity: 0.358 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.5 Details: PEG 600, MgOAc, NaCl, ZnSO4, pH 4.5, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 2, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.191→50 Å / Num. all: 34915 / Num. obs: 34915 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.103 / Χ2: 1.485 / Net I/σ(I): 9.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GTW Resolution: 3.191→49.061 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7904 / SU ML: 0.92 / σ(F): 2.1 / Phase error: 28.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.435 Å2 / ksol: 0.311 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 212.58 Å2 / Biso mean: 98.1188 Å2 / Biso min: 26.93 Å2
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Refinement step | Cycle: LAST / Resolution: 3.191→49.061 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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