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- PDB-6gfg: Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gfg | ||||||
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Title | Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with D-chiro-IP6 and ADP | ||||||
![]() | Inositol-pentakisphosphate 2-kinase![]() | ||||||
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Function / homology | ![]() inositol tetrakisphosphate 2-kinase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Whitfield, H.L. / Brearley, C.A. / Hemmings, A.M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.5 KB | Display | ![]() |
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PDB format | ![]() | 145.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6fjkC ![]() 6fl3C ![]() 6fl8C ![]() 6gfhC ![]() 2xamS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 52863.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: A0A178UAB5, UniProt: Q93YN9*PLUS, ![]() #2: Chemical | #3: Chemical | ![]() #4: Chemical | ChemComp-MG / #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.91 % |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2012 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||
Reflection | Resolution: 3→29.02 Å / Num. obs: 19896 / % possible obs: 96.7 % / Redundancy: 2.3 % / Biso Wilson estimate: 55.76 Å2 / CC1/2: 0.953 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.131 / Rrim(I) all: 0.199 / Net I/σ(I): 7.1 / Num. measured all: 45894 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2XAM Resolution: 3→29.017 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.4 Å2 / Biso mean: 52.4431 Å2 / Biso min: 17.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→29.017 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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