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- PDB-8oxe: Inositol 1,3,4-trisphosphate 5/6-kinase 1 from Solanum tuberosum ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8oxe | ||||||
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Title | Inositol 1,3,4-trisphosphate 5/6-kinase 1 from Solanum tuberosum (StITPK1) in complex with ADP/Mg2+ | ||||||
![]() | Inositol-tetrakisphosphate 1-kinase | ||||||
![]() | TRANSFERASE / Inositol kinase | ||||||
Function / homology | ![]() inositol-tetrakisphosphate 1-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 / inositol trisphosphate metabolic process / phosphorylation / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Faba-Rodriguez, R. / Li, A.W.H. / Brearley, C.A. / Hemmings, A.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure and Enzymology of Solanum tuberosum Inositol Tris/Tetrakisphosphate Kinase 1 ( St ITPK1). Authors: Whitfield, H.L. / Rodriguez, R.F. / Shipton, M.L. / Li, A.W.H. / Riley, A.M. / Potter, B.V.L. / Hemmings, A.M. / Brearley, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.4 KB | Display | ![]() |
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PDB format | ![]() | 110.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 773.3 KB | Display | ![]() |
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Full document | ![]() | 776 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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
#1: Protein | Mass: 36877.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-ADP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2 M calcium chloride dihydrate, 0.1 M MES pH 6.0, 20% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→75.59 Å / Num. obs: 519292 / % possible obs: 99.69 % / Redundancy: 20 % / Biso Wilson estimate: 27.96 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.0434 / Rrim(I) all: 0.2088 / Net I/σ(I): 20.82 |
Reflection shell | Resolution: 2.26→2.34 Å / Redundancy: 15 % / Num. unique obs: 50938 / CC1/2: 0.868 / CC star: 0.964 / % possible all: 99.21 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→75.59 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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