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Yorodumi- PDB-7pup: INOSITOL 1,3,4-TRISPHOSPHATE 5/6-KINASE 4 from Arabidopsis thalia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pup | ||||||
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Title | INOSITOL 1,3,4-TRISPHOSPHATE 5/6-KINASE 4 from Arabidopsis thaliana (AtITPK4) in complex with ATP | ||||||
Components | Inositol 1,3,4-trisphosphate 5/6-kinase 4 | ||||||
Keywords | TRANSFERASE / ATP binding / inositol kinase | ||||||
Function / homology | Function and homology information : / inositol-1,3,4-trisphosphate 5/6-kinase / inositol-3,4,5,6-tetrakisphosphate 1-kinase activity / inositol-1,3,4-trisphosphate 6-kinase activity / inositol-1,3,4-trisphosphate 5-kinase activity / myo-inositol hexakisphosphate biosynthetic process / inositol trisphosphate metabolic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Whitfield, H. / He, S. / Brearley, C.A. / Hemmings, A.M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biochem.J. / Year: 2023 Title: Diversification in the inositol tris/tetrakisphosphate kinase (ITPK) family: crystal structure and enzymology of the outlier AtITPK4. Authors: Whitfield, H.L. / He, S. / Gu, Y. / Sprigg, C. / Kuo, H.F. / Chiou, T.J. / Riley, A.M. / 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 | 7pup.cif.gz | 247.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pup.ent.gz | 165.6 KB | Display | PDB format |
PDBx/mmJSON format | 7pup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pup_validation.pdf.gz | 825 KB | Display | wwPDB validaton report |
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Full document | 7pup_full_validation.pdf.gz | 841.1 KB | Display | |
Data in XML | 7pup_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 7pup_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/7pup ftp://data.pdbj.org/pub/pdb/validation_reports/pu/7pup | HTTPS FTP |
-Related structure data
Related structure data | 1z2nS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54395.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ITPK4, At2g43980, F6E13.11 / Production host: Escherichia coli (E. coli) References: UniProt: O80568, inositol-1,3,4-trisphosphate 5/6-kinase |
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#2: Chemical | ChemComp-ATP / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.28 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000, 0.1M MgCl2, 0.1M Tris pH7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→44.17 Å / Num. obs: 39622 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 33.32 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.0528 / Rrim(I) all: 0.1928 / Net I/σ(I): 10.14 |
Reflection shell | Resolution: 1.91→1.98 Å / Redundancy: 13.1 % / Rmerge(I) obs: 2.965 / Mean I/σ(I) obs: 0.87 / Num. unique obs: 3887 / CC1/2: 0.376 / CC star: 0.739 / Rpim(I) all: 0.842 / Rrim(I) all: 2.808 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Z2N Resolution: 1.91→44.17 Å / SU ML: 0.2336 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1622 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→44.17 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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