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Yorodumi- PDB-2xal: Lead derivative of Inositol 1,3,4,5,6-pentakisphosphate 2-kinase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xal | |||||||||
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Title | Lead derivative of Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with ADP and IP6. | |||||||||
Components | INOSITOL-PENTAKISPHOSPHATE 2-KINASE | |||||||||
Keywords | TRANSFERASE / INOSITOL POLYPHOSPHATE KINASE / PHYTIC ACID SYNTHASE | |||||||||
Function / homology | Function and homology information inositol-1,4,5,6-tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol-1,3,4,5,6-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-1,4,5,6-tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol-1,3,4,5,6-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 / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å | |||||||||
Authors | Gonzalez, B. / Banos-Sanz, J.I. / Villate, M. / Brearley, C.A. / Sanz-Aparicio, J. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase is a Distant Ipk Member with a Singular Inositide Binding Site for Axial 2-Oh Recognition. Authors: Gonzalez, B. / Banos-Sanz, J.I. / Villate, M. / Brearley, C.A. / Sanz-Aparicio, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xal.cif.gz | 182.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xal.ent.gz | 144.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xal_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 2xal_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 2xal_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 2xal_validation.cif.gz | 52.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/2xal ftp://data.pdbj.org/pub/pdb/validation_reports/xa/2xal | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 2
NCS ensembles :
NCS oper: (Code: given Matrix: (0.99776, 0.05526, 0.03759), Vector: |
-Components
#1: Protein | Mass: 50717.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: PKLSLT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLySS References: UniProt: Q93YN9, inositol-pentakisphosphate 2-kinase #2: Chemical | #3: Chemical | ChemComp-PB / #4: Chemical | #5: Chemical | Has protein modification | Y | Sequence details | THERE ARE SEVERAL DISCREPANC | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % Description: HIGH RESOLUTION DATA FROM PDB ENTRY 2XAM WAS NECESARY FOR MODEL COMPLETION AND REFINEMENT |
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Crystal grow | pH: 5.9 Details: 22% PEG 3350, 100 MM BIS-TRIS PH 5.9, SOAKING IN 100 MM LEAD ACETATE. PROTEIN WAS MIXED WITH 2 MM ADP AND 2 MM INOSITOL-6-P |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9478 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9478 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→138.69 Å / Num. obs: 15450 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.68 % / Biso Wilson estimate: 53.8 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.34 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.66 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 3.2→86.71 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.852 / SU B: 44.748 / SU ML: 0.44 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.598 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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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: 21.91 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→86.71 Å
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Refine LS restraints |
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