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Yorodumi- PDB-3mtc: Crystal Structure of INPP5B in complex with phosphatidylinositol ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mtc | ||||||
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Title | Crystal Structure of INPP5B in complex with phosphatidylinositol 4-phosphate | ||||||
Components | Type II inositol-1,4,5-trisphosphate 5-phosphatase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / INPP5BA / Phosphoinositide 5-phosphatase / inositol signalling / phosphatase / magnesium / structural genomics / SGC / SGC Stockholm / Structural Genomics Consortium / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / flagellated sperm motility / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / regulation of protein processing / Synthesis of IP3 and IP4 in the cytosol ...Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / flagellated sperm motility / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / regulation of protein processing / Synthesis of IP3 and IP4 in the cytosol / endoplasmic reticulum-Golgi intermediate compartment / phagocytic vesicle membrane / early endosome membrane / spermatogenesis / in utero embryonic development / Golgi apparatus / signal transduction / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Structure / Year: 2014 Title: Structural basis for phosphoinositide substrate recognition, catalysis, and membrane interactions in human inositol polyphosphate 5-phosphatases Authors: Tresaugues, L. / Silvander, C. / Flodin, S. / Welin, M. / Nyman, T. / Graslund, S. / Hammarstrom, M. / Berglund, H. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mtc.cif.gz | 86 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mtc.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 3mtc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/3mtc ftp://data.pdbj.org/pub/pdb/validation_reports/mt/3mtc | HTTPS FTP |
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-Related structure data
Related structure data | 3n9vC 3nr8C 4cmlC 4cmnC 1i9yS 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36201.086 Da / Num. of mol.: 1 / Fragment: UNP residues 339-643 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INPP5B / Plasmid: pNIC-CH2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) R3 pRARE / References: UniProt: P32019, phosphoinositide 5-phosphatase |
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-Non-polymers , 6 types, 231 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-PIF / ( | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-CL / | #7: 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: 5.51 Å3/Da / Density % sol: 77.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 22% polyacrylic acid, 0.02M magnesium chloride, 0.1M hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97908 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2009 / Details: mirrors |
Radiation | Monochromator: Si(311) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→94.51 Å / Num. all: 31433 / Num. obs: 31380 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2 / Num. unique all: 4498 / Rsym value: 0.698 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I9Y Resolution: 2.4→47.29 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.057 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R Free: 0.155 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.796 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→47.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.463 Å / Total num. of bins used: 20
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