+Open data
-Basic information
Entry | Database: PDB / ID: 8fvz | ||||||
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Title | PiPT Y150A | ||||||
Components | Phosphate transporterPhosphate permease | ||||||
Keywords | TRANSPORT PROTEIN / Major facilitator / phosphate transport / membrane protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Serendipita indica (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Gupta, M. / Finer-Moore, J. / Stroud, R.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Roles of PiPT residues in phosphate binding and transport tested by mutagenesis Authors: Gupta, M. / Finer-Moore, J. / Nelson, A. / Kumar, H. / Verma, N. / Jhori, A. / Stroud, R.M. #1: Journal: Nature / Year: 2013 Title: Crystal structure of a eukaryotic phosphate transporter. Authors: Pedersen, B.P. / Kumar, H. / Waight, A.B. / Risenmay, A.J. / Roe-Zurz, Z. / Chau, B.H. / Schlessinger, A. / Bonomi, M. / Harries, W. / Sali, A. / Johri, A.K. / Stroud, R.M. #2: Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Key computational findings reveal proton transfer as driving the functional cycle in the phosphate transporter PiPT. Authors: Liu, Y. / Li, C. / Gupta, M. / Verma, N. / Johri, A.K. / Stroud, R.M. / Voth, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fvz.cif.gz | 179.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fvz.ent.gz | 140.2 KB | Display | PDB format |
PDBx/mmJSON format | 8fvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/8fvz ftp://data.pdbj.org/pub/pdb/validation_reports/fv/8fvz | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58446.570 Da / Num. of mol.: 2 / Mutation: Y150A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serendipita indica (fungus) / Plasmid: PRS423-GAL1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): DSY-5 / References: UniProt: A8N031 #2: Chemical | #3: Chemical | ChemComp-FLC / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 4.3 Å3/Da / Density % sol: 72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 27%(w/v) pentaerythritol propoxylate, 5% polyethylene glycol 400, .2M KCL, .1M sodium citrate pH5.5 |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11584 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.11584 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→48 Å / Num. obs: 34818 / % possible obs: 100 % / Redundancy: 10.54 % / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.163 / Net I/σ(I): 11.59 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→47.76 Å / Cross valid method: FREE R-VALUE / σ(F): 422.77 / Phase error: 43.81 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→47.76 Å
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Refine LS restraints |
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LS refinement shell |
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