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Yorodumi- PDB-6fl8: Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fl8 | ||||||
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Title | Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with purpurogallin and ADP | ||||||
Components | Inositol-pentakisphosphate 2-kinase | ||||||
Keywords | TRANSFERASE / IPK1 / PURPUROGALLIN / ADP | ||||||
Function / homology | Function and homology information inositol-1,4,5,6-tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol-1,3,4,5,6-pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / inositol phosphate biosynthetic process / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / phosphorylation ...inositol-1,4,5,6-tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol-1,3,4,5,6-pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / inositol phosphate biosynthetic process / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / phosphorylation / defense response to virus / defense response to bacterium / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Whitfield, H.L. / Brearley, C.A. / Hemmings, A.M. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: A Fluorescent Probe Identifies Active Site Ligands of Inositol Pentakisphosphate 2-Kinase. Authors: Whitfield, H. / Gilmartin, M. / Baker, K. / Riley, A.M. / Godage, H.Y. / Potter, B.V.L. / Hemmings, A.M. / Brearley, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fl8.cif.gz | 195.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fl8.ent.gz | 151.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fl8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/6fl8 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/6fl8 | HTTPS FTP |
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-Related structure data
Related structure data | 6fjkC 6fl3C 6gfgC 6gfhC 2xamS 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: 52863.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At5g40720 / Production host: Escherichia coli (E. coli) References: UniProt: A0A178UAB5, UniProt: Q93YN9*PLUS, inositol-pentakisphosphate 2-kinase |
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-Non-polymers , 7 types, 280 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-TRS / | #8: 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: 2.57 Å3/Da / Density % sol: 52.11 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18 % PEG 3350, 0.1 M bis-tris propane pH 6.5, 2 mM MgCl2, 25% EG or 35% PEG 3350, 0.1 M bis-tris propane pH 6.5, 2 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 6, 2016 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.1→54.29 Å / Num. obs: 55908 / % possible obs: 91 % / Redundancy: 2.3 % / Biso Wilson estimate: 38.53 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.066 / Rrim(I) all: 0.104 / Net I/σ(I): 6.3 / Num. measured all: 129143 / Scaling rejects: 1 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2.3 %
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XAM Resolution: 2.1→54.295 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→54.295 Å
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Refine LS restraints |
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LS refinement shell |
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