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Yorodumi- PDB-4aqk: Inositol 1,3,4,5,6-pentakisphosphate 2-kinase in complex with ADP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aqk | |||||||||
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Title | Inositol 1,3,4,5,6-pentakisphosphate 2-kinase in complex with ADP and IP6 | |||||||||
Components | INOSITOL-PENTAKISPHOSPHATE 2-KINASE | |||||||||
Keywords | TRANSFERASE / INOSITIDE KINASE / PHYTIC ACID / INOSITIDE SIGNALLING / INSP5 2-K | |||||||||
Function / homology | Function and homology information inositol tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / defense response to virus / defense response to bacterium ...inositol tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / defense response to virus / defense response to bacterium / phosphorylation / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | I Banos-Sanz, J. / Sanz-Aparicio, J. / Gonzalez, B. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Expression, Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of the Apo Form of Insp5 2-K from Arabidopsis Thaliana. Authors: Banos-Sanz, J.I. / Sanz-Aparicio, J. / Brearley, C.A. / Gonzalez, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aqk.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aqk.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 4aqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/4aqk ftp://data.pdbj.org/pub/pdb/validation_reports/aq/4aqk | HTTPS FTP |
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-Related structure data
Related structure data | 2xanS S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 51321.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS References: UniProt: Q93YN9, inositol-pentakisphosphate 2-kinase |
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-Non-polymers , 5 types, 64 molecules
#2: Chemical | ChemComp-IHP / |
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#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-ZN / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.77 % / Description: NONE |
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Crystal grow | pH: 5.9 / Details: 22% PEG 3350, BIS-TRIS PH 5.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 9, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→62.11 Å / Num. obs: 20463 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.1 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XAN Resolution: 2.4→60.9 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.852 / SU B: 11.004 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.522 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.452 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→60.9 Å
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