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Yorodumi- PDB-5dgh: Crystal structure of the catalytic domain of human diphosphoinosi... -
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-Basic information
Entry | Database: PDB / ID: 5dgh | ||||||
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Title | Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCP)-IP5 | ||||||
Components | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | ||||||
Keywords | TRANSFERASE / TRANSFERASE Inositol diphosphoinositol pentakisphosphate kinase Analog methylenebisphosphonate PPIP5K ATP-grasp Pyrophosphate Diphosphate | ||||||
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 / inositol hexakisphosphate kinase activity / Synthesis of pyrophosphates in the cytosol / 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 / inositol hexakisphosphate kinase activity / Synthesis of pyrophosphates in the cytosol / inositol phosphate metabolic process / inositol phosphate biosynthetic process / inositol metabolic process / sensory perception of sound / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Wang, H. / Shears, S.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chemistry / Year: 2016 Title: Cellular Cations Control Conformational Switching of Inositol Pyrophosphate Analogues. Authors: Hager, A. / Wu, M. / Wang, H. / Brown, N.W. / Shears, S.B. / Veiga, N. / Fiedler, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dgh.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dgh.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 5dgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dgh_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5dgh_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5dgh_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 5dgh_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/5dgh ftp://data.pdbj.org/pub/pdb/validation_reports/dg/5dgh | HTTPS FTP |
-Related structure data
Related structure data | 5dgiC 3t7aS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37568.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPIP5K2, HISPPD1, KIAA0433, VIP2 / Plasmid: pDest566 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Arctic Express (DE3) References: UniProt: O43314, inositol-hexakisphosphate 5-kinase, diphosphoinositol-pentakisphosphate 1-kinase |
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-Non-polymers , 6 types, 281 molecules
#2: Chemical | ChemComp-ANP / | ||||||
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#3: Chemical | ChemComp-5A3 / | ||||||
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMP-PNP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M ...Details: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMP-PNP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M sodium acetate, pH 5.2 at 4 oC overnight. The crystals were soaked under the above stabilizing buffer for three days with 2 mM compound. |
-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: Jun 12, 2015 |
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. obs: 23365 / % possible obs: 96.8 % / Redundancy: 4.8 % / Rsym value: 0.083 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.1→2.35 Å / Redundancy: 3 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.5 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3T7A Resolution: 2.1→29.04 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.275 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.184 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.654 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→29.04 Å
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