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Yorodumi- PDB-4o4c: Crystal Structure of an Inositol hexakisphosphate kinase apo-EhIP6KA -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o4c | ||||||
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Title | Crystal Structure of an Inositol hexakisphosphate kinase apo-EhIP6KA | ||||||
Components | Inositol hexakisphosphate kinase | ||||||
Keywords | TRANSFERASE / PDKG 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: 2.2 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 | 4o4c.cif.gz | 212 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o4c.ent.gz | 170.3 KB | Display | PDB format |
PDBx/mmJSON format | 4o4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/4o4c ftp://data.pdbj.org/pub/pdb/validation_reports/o4/4o4c | HTTPS FTP |
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-Related structure data
Related structure data | 4o4bSC 4o4dC 4o4eC 4o4fC 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: 0 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 30 - 270 / Label seq-ID: 15 - 255
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-Components
#1: Protein | Mass: 29899.193 Da / Num. of mol.: 2 / Fragment: UNP residues 20-270 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 #2: 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: 2.23 Å3/Da / Density % sol: 44.89 % |
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Crystal grow | Temperature: 298 K / Method: micro seeding / pH: 5.2 Details: 8% (w/v) PEG 3350, 100 mM Na3Citrate, pH 5.2 at 25C, Micro Seeding, temperature 298K |
-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 28, 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: 1.9→50 Å / Num. obs: 25151 / % possible obs: 98.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.078 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 1927 / Rsym value: 0.235 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4O4B Resolution: 2.2→32.11 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.839 / SU B: 13.702 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.388 / ESU R Free: 0.267 / 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: 25.328 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→32.11 Å
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Refine LS restraints |
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