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Yorodumi- PDB-5dlv: Crystal structure of Autotaxin (ENPP2) with tauroursodeoxycholic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dlv | |||||||||
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Title | Crystal structure of Autotaxin (ENPP2) with tauroursodeoxycholic acid (TUDCA) | |||||||||
Components | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | |||||||||
Keywords | HYDROLASE / Autotaxin / ENPP2 / LPA / steroids / bile salts / TUDCA | |||||||||
Function / homology | Function and homology information response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity ...response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity / polysaccharide binding / positive regulation of oligodendrocyte differentiation / negative regulation of cell-matrix adhesion / 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 / regulation of cell migration / cellular response to cadmium ion / cell chemotaxis / cellular response to estradiol stimulus / positive regulation of peptidyl-tyrosine phosphorylation / nucleic acid binding / immune response / calcium ion binding / positive regulation of cell population proliferation / extracellular space / zinc ion binding Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Keune, W.J. / Heidebrecht, T. / von Castelmur, E. / Joosten, R.P. / Perrakis, A. | |||||||||
Funding support | Netherlands, 2items
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Citation | Journal: Nat Commun / Year: 2016 Title: Steroid binding to Autotaxin links bile salts and lysophosphatidic acid signalling. Authors: Keune, W.J. / Hausmann, J. / Bolier, R. / Tolenaars, D. / Kremer, A. / Heidebrecht, T. / Joosten, R.P. / Sunkara, M. / Morris, A.J. / Matas-Rico, E. / Moolenaar, W.H. / Oude Elferink, R.P. / Perrakis, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dlv.cif.gz | 674.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dlv.ent.gz | 555.2 KB | Display | PDB format |
PDBx/mmJSON format | 5dlv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/5dlv ftp://data.pdbj.org/pub/pdb/validation_reports/dl/5dlv | HTTPS FTP |
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-Related structure data
Related structure data | 5dltC 5dlwC 2xr9S C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 56 - 859 / Label seq-ID: 21 - 824
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 95003.641 Da / Num. of mol.: 2 / Mutation: N53A, N410A, N806A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: c / Cell line (production host): HEK293 / Production host: Homo sapiens (human) References: UniProt: Q64610, alkylglycerophosphoethanolamine phosphodiesterase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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 | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-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 |
-Non-polymers , 9 types, 643 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | #6: Chemical | ChemComp-IOD / #7: Chemical | #8: Chemical | ChemComp-NA / #9: Chemical | #10: Chemical | ChemComp-SCN / #11: Chemical | ChemComp-GOL / #12: Water | ChemComp-HOH / | |
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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: 2.27 Å3/Da / Density % sol: 45.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.3M sodium thiocyanate, 0.2 ammonium iodide, 350 uM TUDCA |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87257 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 21, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.87257 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2→46.79 Å / Num. obs: 110991 / % possible obs: 97.9 % / Redundancy: 3.6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.109 / Net I/σ(I): 5.6 / Num. measured all: 396989 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2xr9 Resolution: 2→90.61 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / Matrix type: sparse / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.174 / SU B: 12.655 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.37 Å2 / Biso mean: 35.513 Å2 / Biso min: 12.99 Å2
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Refinement step | Cycle: final / Resolution: 2→90.61 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 97182 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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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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