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Yorodumi- PDB-5y79: Crystal structure of the triose-phosphate/phosphate translocator ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y79 | ||||||
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Title | Crystal structure of the triose-phosphate/phosphate translocator in complex with 3-phosphoglycerate | ||||||
Components | Putative hexose phosphate translocator | ||||||
Keywords | TRANSPORT PROTEIN / Chloroplast / inner envelop membrane / antiporter / sugar phosphate | ||||||
Function / homology | Sugar phosphate transporter domain / Triose-phosphate Transporter family / membrane / 3-PHOSPHOGLYCERIC ACID / CITRATE ANION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Putative hexose phosphate translocator Function and homology information | ||||||
Biological species | Galdieria sulphuraria (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lee, Y. / Nishizawa, T. / Takemoto, M. / Kumazaki, K. / Yamashita, K. / Hirata, K. / Minoda, A. / Nagatoishi, S. / Tsumoto, K. / Ishitani, R. / Nureki, O. | ||||||
Citation | Journal: Nat Plants / Year: 2017 Title: Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity Authors: Lee, Y. / Nishizawa, T. / Takemoto, M. / Kumazaki, K. / Yamashita, K. / Hirata, K. / Minoda, A. / Nagatoishi, S. / Tsumoto, K. / Ishitani, R. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y79.cif.gz | 150.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y79.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 5y79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/5y79 ftp://data.pdbj.org/pub/pdb/validation_reports/y7/5y79 | HTTPS FTP |
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-Related structure data
Related structure data | 5y78C 5i20S 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: 36575.195 Da / Num. of mol.: 2 / Fragment: UNP residues 91-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Galdieria sulphuraria (eukaryote) / Gene: Gasu_48050, Gs48050.1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B5AJT1 #2: Chemical | ChemComp-OLC / ( #3: Chemical | #4: Chemical | ChemComp-FLC / | #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: 2.49 Å3/Da / Density % sol: 50.57 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 / Details: PEG200, Na-citrate, 3K-citrate, 2Na(3-PGA) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 38123 / % possible obs: 100 % / Redundancy: 39.2 % / CC1/2: 0.994 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 27 % / Mean I/σ(I) obs: 1.3 / CC1/2: 0.698 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I20 Resolution: 2.2→48.998 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→48.998 Å
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Refine LS restraints |
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LS refinement shell |
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