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Yorodumi- PDB-5w2h: Crystal structure of the core catalytic domain of human inositol ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w2h | ||||||||||||
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Title | Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with Ins(1,4,5)P3 and ADP | ||||||||||||
Components | Inositol polyphosphate multikinase,Inositol polyphosphate multikinase | ||||||||||||
Keywords | TRANSFERASE / kinase / inositol / inositol polyphosphate / phosphatidylinositol / specificity | ||||||||||||
Function / homology | Function and homology information Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol tetrakisphosphate 5-kinase activity / myo-inositol-1,2,3,4,6-heptakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol tetrakisphosphate 3-kinase activity / flavonoid binding / inositol tetrakisphosphate 6-kinase activity / inositol tetrakisphosphate kinase activity ...Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol tetrakisphosphate 5-kinase activity / myo-inositol-1,2,3,4,6-heptakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol tetrakisphosphate 3-kinase activity / flavonoid binding / inositol tetrakisphosphate 6-kinase activity / inositol tetrakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / inositol trisphosphate metabolic process / inositol phosphate metabolic process / inositol phosphate biosynthetic process / phosphatidylinositol metabolic process / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / necroptotic process / phosphorylation / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||||||||
Authors | Wang, H. / Shears, S.B. | ||||||||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Structural features of human inositol phosphate multikinase rationalize its inositol phosphate kinase and phosphoinositide 3-kinase activities. Authors: Wang, H. / Shears, S.B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w2h.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w2h.ent.gz | 99 KB | Display | PDB format |
PDBx/mmJSON format | 5w2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/5w2h ftp://data.pdbj.org/pub/pdb/validation_reports/w2/5w2h | HTTPS FTP |
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-Related structure data
Related structure data | 5w2gSC 5w2iC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29427.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IPMK, IMPK / Production host: Escherichia coli (E. coli) References: UniProt: Q8NFU5, inositol-polyphosphate multikinase |
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-Non-polymers , 5 types, 177 molecules
#2: Chemical | #3: Chemical | ChemComp-ADP / | #4: Chemical | ChemComp-I3P / | #5: Chemical | ChemComp-PO4 / | #6: 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: 2.22 Å3/Da / Density % sol: 44.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol.To obtain complex structures, the apo crystal were further soaked under 35% (w/v) PEG 400, 0. ...Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol.To obtain complex structures, the apo crystal were further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 20 mM Ins(1,4,5)P3, 10 mM Mg and 5mM ATP for 1 day. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 21557 / % possible obs: 99.9 % / Redundancy: 9 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 3.3 / Rpim(I) all: 0.317 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5W2G Resolution: 1.9→32.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.256 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R Free: 0.15 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.704 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→32.35 Å
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Refine LS restraints |
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