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Yorodumi- PDB-3t9b: Crystal structure of the catalytic domain of human diphosphoinosi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t9b | ||||||
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Title | Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP at pH 5.2 | ||||||
Components | Inositol Pyrophosphate Kinase | ||||||
Keywords | TRANSFERASE / ATP-grasp Fold / Inositol Pyrophosphate Kinase / Phosphoryl Transferase | ||||||
Function / homology | Function and homology information diphosphoinositol-pentakisphosphate 1-kinase / diphosphoinositol pentakisphosphate kinase activity / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate 5-kinase activity / Synthesis of pyrophosphates in the cytosol / inositol hexakisphosphate kinase activity / inositol phosphate metabolic process ...diphosphoinositol-pentakisphosphate 1-kinase / diphosphoinositol pentakisphosphate kinase activity / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate 5-kinase activity / Synthesis of pyrophosphates in the cytosol / inositol hexakisphosphate kinase activity / inositol phosphate metabolic process / inositol phosphate biosynthetic process / inositol metabolic process / sensory perception of sound / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å | ||||||
Authors | Wang, H. / Falck, J. / Hall, T.M.T. / Shears, S.B. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2011 Title: Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding. Authors: Wang, H. / Falck, J.R. / Hall, T.M. / 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 | 3t9b.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t9b.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 3t9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t9b_validation.pdf.gz | 775.6 KB | Display | wwPDB validaton report |
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Full document | 3t9b_full_validation.pdf.gz | 776.2 KB | Display | |
Data in XML | 3t9b_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 3t9b_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/3t9b ftp://data.pdbj.org/pub/pdb/validation_reports/t9/3t9b | HTTPS FTP |
-Related structure data
Related structure data | 3t54C 3t7aC 3t99C 3t9aC 3t9cC 3t9dC 3t9eC 3t9fC 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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Unit cell |
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-Components
#1: Protein | Mass: 37568.891 Da / Num. of mol.: 1 / Fragment: ATP-grasp Kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPIP5K2 / Plasmid: pDest566 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express (DE3) References: UniProt: O43314, diphosphoinositol-pentakisphosphate 1-kinase | ||
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#2: Chemical | ChemComp-ANP / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMPPNP, 2 mM CdCl2, Soaking under pH 5.2 for 2 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-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2011 |
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: 1.85→50 Å / Num. obs: 35550 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rsym value: 0.12 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.48 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→35.44 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 16.723 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→35.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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