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Yorodumi- PDB-4axd: Inositol 1,3,4,5,6-pentakisphosphate 2-kinase in complex with AMPPNP -
+Open data
-Basic information
Entry | Database: PDB / ID: 4axd | ||||||
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Title | Inositol 1,3,4,5,6-pentakisphosphate 2-kinase in complex with AMPPNP | ||||||
Components | INOSITOL-PENTAKISPHOSPHATE 2-KINASE | ||||||
Keywords | TRANSFERASE / INOSITOL KINASE / PHYTIC ACID / PROTEIN KINASE / INOSITIDE SIGNALLING | ||||||
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: 2.05 Å | ||||||
Authors | I Banos-Sanz, J. / Sanz-Aparicio, J. / Gonzalez, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Conformational Changes Undergone by Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase Upon Substrate Binding: The Role of N-Lobe and Enantiomeric Substrate Preference Authors: Banos-Sanz, J.I. / Sanz-Aparicio, J. / Whitfield, H. / Hamilton, C. / 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 | 4axd.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4axd.ent.gz | 83.2 KB | Display | PDB format |
PDBx/mmJSON format | 4axd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/4axd ftp://data.pdbj.org/pub/pdb/validation_reports/ax/4axd | HTTPS FTP |
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-Related structure data
Related structure data | 4axcC 4axeC 4axfC 2xanS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 51206.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICIA 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, 329 molecules
#2: Chemical | ChemComp-ANP / | ||||
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#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CIT / | #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: 2.24 Å3/Da / Density % sol: 45.03 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: 0.5 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 0.8 M LISO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1.0053 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0053 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→53.37 Å / Num. obs: 29280 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XAN Resolution: 2.05→53.37 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→53.37 Å
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Refine LS restraints |
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