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Yorodumi- PDB-5ijj: Structure of the SPX domain of Chaetomium thermophilum Glyceropho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ijj | |||||||||
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Title | Structure of the SPX domain of Chaetomium thermophilum Glycerophosphodiester Phosphodiesterase 1 in complex with inositol hexakisphosphate (InsP6) | |||||||||
Components | SPX domain | |||||||||
Keywords | inositol polyphosphate binding protein / helical bundle / alpha-helical hairpin / inositol phosphate binding / protein-protein interaction / Hydrolase | |||||||||
Function / homology | Function and homology information glycerophosphocholine phosphodiesterase activity / glycerophospholipid catabolic process / cytoplasm Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Wild, R. / Hothorn, M. | |||||||||
Funding support | Switzerland, 1items
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Citation | Journal: Science / Year: 2016 Title: Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains. Authors: Wild, R. / Gerasimaite, R. / Jung, J.Y. / Truffault, V. / Pavlovic, I. / Schmidt, A. / Saiardi, A. / Jessen, H.J. / Poirier, Y. / Hothorn, M. / Mayer, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ijj.cif.gz | 154.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ijj.ent.gz | 122.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ijj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/5ijj ftp://data.pdbj.org/pub/pdb/validation_reports/ij/5ijj | HTTPS FTP |
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-Related structure data
Related structure data | 5iigSC 5iiqC 5iitC 5ijhC 5ijpC 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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-Components
#1: Protein | Mass: 22286.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0005190 / Plasmid: pMH-HC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL References: UniProt: G0RY29, glycerophosphodiester phosphodiesterase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-ACT / | #5: 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: 2.31 Å3/Da / Density % sol: 46.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG 3350, 0.1M ammonium acetate, 0.1M BisTris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 28959 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 41 Å2 / CC1/2: 1 / Rsym value: 0.06 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.95→2.07 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.28 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IIG Resolution: 1.95→19.59 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.211 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.163 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.756 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→19.59 Å
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Refine LS restraints |
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