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Yorodumi- PDB-1u2t: X-Ray structure of the sucrose-phosphatase (SPP) from Synechocyst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u2t | |||||||||
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Title | X-Ray structure of the sucrose-phosphatase (SPP) from Synechocystis sp. PCC6803 in complex with sucrose6P | |||||||||
Components | sucrose-phosphatase (SPP) | |||||||||
Keywords | HYDROLASE / phosphohydrolase / HAD superfamily / sucrose / sucrose6P / 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: 2.9 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 | 1u2t.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u2t.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 1u2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u2t_validation.pdf.gz | 820.9 KB | Display | wwPDB validaton report |
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Full document | 1u2t_full_validation.pdf.gz | 826.3 KB | Display | |
Data in XML | 1u2t_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 1u2t_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/1u2t ftp://data.pdbj.org/pub/pdb/validation_reports/u2/1u2t | HTTPS FTP |
-Related structure data
Related structure data | 1s2oC 1tj3SC 1tj4C 1tj5C 1u2sC C: citing same article (ref.) S: Starting model for refinement |
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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 | 6-O-phosphono-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose-6-phosphate |
#3: 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: 3.31 Å3/Da / Density % sol: 62.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: NaFormate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 5, 2004 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 8968 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.203 / Rsym value: 0.203 / Net I/σ(I): 12.96 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body Starting model: PDB ENTRY 1TJ3 Resolution: 2.9→50 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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