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Yorodumi- PDB-2xan: inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xan | ||||||
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Title | inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with AMP PNP and IP5 | ||||||
Components | INOSITOL-PENTAKISPHOSPHATE 2-KINASE | ||||||
Keywords | TRANSFERASE / PHYTIC ACID SYNTHASE / IP6 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 2xan.cif.gz | 186 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xan.ent.gz | 146 KB | Display | PDB format |
PDBx/mmJSON format | 2xan.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/2xan ftp://data.pdbj.org/pub/pdb/validation_reports/xa/2xan | HTTPS FTP |
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-Related structure data
Related structure data | 2xalC 2xamSC 2xaoC 2xarC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
NCS oper: (Code: given Matrix: (0.99907, 0.04084, 0.01363), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 267 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 5.9 Details: 22% PEG 3350, 100 MM BIS-TRIS, PH 5.9 PROTEIN WAS MIXED WITH 2 MM AMP PNP AND 2 MM INOSITOL-5-P |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→88.25 Å / Num. obs: 47247 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.6 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XAM Resolution: 2.2→140.03 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.885 / SU B: 12.962 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.246 / 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: 21.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→140.03 Å
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Refine LS restraints |
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