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Yorodumi- PDB-4o4d: Crystal Structure of an Inositol hexakisphosphate kinase EhIP6KA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o4d | ||||||
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Title | Crystal Structure of an Inositol hexakisphosphate kinase EhIP6KA in complexed with ATP and Ins(1,4,5)P3 | ||||||
Components | Inositol hexakisphosphate kinase | ||||||
Keywords | TRANSFERASE / PDGK Kinase / Inositol Phosphate | ||||||
Function / homology | Function and homology information Transferases; Transferring phosphorus-containing groups / inositol phosphate biosynthetic process / kinase activity / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wang, H. / Shears, S.B. | ||||||
Citation | Journal: Nat Commun / Year: 2014 Title: IP6K structure and the molecular determinants of catalytic specificity in an inositol phosphate kinase family. Authors: Wang, H. / DeRose, E.F. / London, R.E. / Shears, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o4d.cif.gz | 127 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o4d.ent.gz | 96.7 KB | Display | PDB format |
PDBx/mmJSON format | 4o4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/4o4d ftp://data.pdbj.org/pub/pdb/validation_reports/o4/4o4d | HTTPS FTP |
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-Related structure data
Related structure data | 4o4bC 4o4cSC 4o4eC 4o4fC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29364.656 Da / Num. of mol.: 1 / Fragment: UNP residues 27-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EHI7A_103520 / Plasmid: pDest566 / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress (DE3) References: UniProt: N9UNA8, inositol-hexakisphosphate 5-kinase |
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-Non-polymers , 6 types, 195 molecules
#2: Chemical | #3: Chemical | ChemComp-I3P / | #4: Chemical | ChemComp-ATP / | #5: Chemical | ChemComp-PO4 / | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
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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: 2.51 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 0.4 M NaH2PO4 in the presence of 10 mM ATP,5 mM IP3, 20 mM MgCl2. The crystals were further soaked under 22% (w/v) PEG 3350, 10 mM MgCl2, 10 mM ATP, 0.1 M sodium acetate, pH 5.2, 10 mM IP3 ...Details: 0.4 M NaH2PO4 in the presence of 10 mM ATP,5 mM IP3, 20 mM MgCl2. The crystals were further soaked under 22% (w/v) PEG 3350, 10 mM MgCl2, 10 mM ATP, 0.1 M sodium acetate, pH 5.2, 10 mM IP3 for 3 days. , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 3, 2013 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 17674 / Num. obs: 17674 / % possible obs: 99.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rsym value: 0.086 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 875 / Rsym value: 0.551 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 4O4C Resolution: 2.1→44.33 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.1 / SU ML: 0.11 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.181 / 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: 39.271 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→44.33 Å
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Refine LS restraints |
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