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- PDB-2xar: 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: 2xar | |||||||||
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Title | Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with IP6. | |||||||||
![]() | INOSITOL-PENTAKISPHOSPHATE 2-KINASE | |||||||||
![]() | TRANSFERASE / IPK / INSP5 2-K / PHYTIC ACID SYNTHASE | |||||||||
Function / homology | ![]() 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 / phosphorylation / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gonzalez, B. / Banos-Sanz, J.I. / Villate, M. / Brearley, C.A. / Sanz-Aparicio, J. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 339.3 KB | Display | ![]() |
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PDB format | ![]() | 280.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 30.8 KB | Display | |
Data in CIF | ![]() | 41.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xalC ![]() 2xamSC ![]() 2xanC ![]() 2xaoC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
NCS oper: (Code: given Matrix: (0.99869, 0.04544, 0.02363), Vector: |
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Components
#1: Protein | Mass: 50717.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q93YN9, inositol-pentakisphosphate 2-kinase #2: Chemical | #3: Chemical | Sequence details | THERE ARE SEVERAL DISCREPANC | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.78 % / Description: NONE |
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Crystal grow | pH: 5.9 Details: 22% PEG 3350, 100 MM BIS-TRIS PH 5.9 2MM MGCL2. PROTEIN WAS MIXED WITH 2 MM INOSITOL-6-P |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→112.5 Å / Num. obs: 17187 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.63 % / Biso Wilson estimate: 67.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.76 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.78 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XAM Resolution: 3.1→112.5 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.838 / SU B: 56.369 / SU ML: 0.486 / Cross valid method: THROUGHOUT / ESU R Free: 0.607 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
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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: 32 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→112.5 Å
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Refine LS restraints |
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