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Yorodumi- PDB-5iig: Structure of the SPX-TTM domain fragment of the yeast inorganic p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iig | ||||||
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Title | Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form A). | ||||||
Components | Vacuolar transporter chaperone 4 | ||||||
Keywords | TRANSFERASE / helical bundle / alpha-helical hairpin / inositol phosphate binding / protein-protein interaction / chaperone | ||||||
Function / homology | Function and homology information vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / microautophagy / vacuole fusion, non-autophagic / polyphosphate metabolic process / inositol hexakisphosphate binding / vacuolar transport ...vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / microautophagy / vacuole fusion, non-autophagic / polyphosphate metabolic process / inositol hexakisphosphate binding / vacuolar transport / vacuolar membrane / fungal-type vacuole membrane / autophagosome membrane / cell periphery / cell cortex / cytoplasmic vesicle / calmodulin binding / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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 | 5iig.cif.gz | 207.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iig.ent.gz | 168.9 KB | Display | PDB format |
PDBx/mmJSON format | 5iig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iig_validation.pdf.gz | 447 KB | Display | wwPDB validaton report |
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Full document | 5iig_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 5iig_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 5iig_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/5iig ftp://data.pdbj.org/pub/pdb/validation_reports/ii/5iig | HTTPS FTP |
-Related structure data
Related structure data | 5iiqC 5iitC 5ijhC 5ijjC 5ijpC 3g3rS 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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Unit cell |
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-Components
#1: Protein | Mass: 56936.605 Da / Num. of mol.: 1 / Fragment: SPX domain, UNP residues 2-480 / Mutation: E426N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VTC4, PHM3, YJL012C, J1345 / Plasmid: pMH-HT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P47075 |
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#2: Chemical | ChemComp-SO4 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 1.5M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→50 Å / Num. obs: 16084 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 119.79 Å2 / CC1/2: 1 / Rsym value: 0.082 / Net I/σ(I): 20.22 |
Reflection shell | Resolution: 2.99→3.17 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3g3r Resolution: 2.99→48.22 Å / Cor.coef. Fo:Fc: 0.9301 / Cor.coef. Fo:Fc free: 0.9285 / SU R Cruickshank DPI: 1.852 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.006 / SU Rfree Blow DPI: 0.394 / SU Rfree Cruickshank DPI: 0.401
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Displacement parameters | Biso mean: 113.86 Å2
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Refine analyze | Luzzati coordinate error obs: 0.7 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.99→48.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.99→3.2 Å / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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