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Yorodumi- PDB-1tj5: X-Ray structure of the Sucrose-Phosphatase (SPP) from Synechocyst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tj5 | |||||||||
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Title | X-Ray structure of the Sucrose-Phosphatase (SPP) from Synechocystis sp. PCC6803 in complex with sucrose and phosphate | |||||||||
Components | Sucrose-Phosphatase | |||||||||
Keywords | HYDROLASE / phosphohydrolase / HAD superfamily / sucrose / cyanobacteria | |||||||||
Function / homology | Function and homology information sucrose-phosphate phosphatase / sucrose-phosphate phosphatase activity / sucrose biosynthetic process / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / rigid body / Resolution: 2.2 Å | |||||||||
Authors | Fieulaine, S. / Lunn, J.E. / Borel, F. / Ferrer, J.-L. | |||||||||
Citation | Journal: Plant Cell / Year: 2005 Title: The structure of a cyanobacterial sucrose-phosphatase reveals the sugar tongs that release free sucrose in the cell. Authors: Fieulaine, S. / Lunn, J.E. / Borel, F. / Ferrer, J.-L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tj5.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tj5.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 1tj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tj5_validation.pdf.gz | 952.8 KB | Display | wwPDB validaton report |
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Full document | 1tj5_full_validation.pdf.gz | 956.6 KB | Display | |
Data in XML | 1tj5_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 1tj5_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/1tj5 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/1tj5 | HTTPS FTP |
-Related structure data
Related structure data | 1s2oC 1tj3SC 1tj4C 1u2sC 1u2tC 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: 27789.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC6803 / Gene: spp / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P74325, sucrose-phosphate phosphatase | ||
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#2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose | ||
#3: Chemical | ChemComp-PO4 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: sodium Formate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 19, 2004 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 19930 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.195 / Rsym value: 0.195 / Net I/σ(I): 10.69 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body Starting model: pdb entry 1TJ3 Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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