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Yorodumi- PDB-2r66: Complex Structure of Sucrose Phosphate Synthase (SPS)-F6P of Halo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r66 | ||||||
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Title | Complex Structure of Sucrose Phosphate Synthase (SPS)-F6P of Halothermothrix orenii | ||||||
Components | Glycosyl transferase, group 1 | ||||||
Keywords | TRANSFERASE / Rossmann-fold | ||||||
Function / homology | Function and homology information sucrose-phosphate synthase / sucrose-phosphate synthase activity / sucrose synthase activity / sucrose metabolic process Similarity search - Function | ||||||
Biological species | Halothermothrix orenii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Sivaraman, J. / Chua, T.K. | ||||||
Citation | Journal: Plant Cell / Year: 2008 Title: The Structure of Sucrose Phosphate Synthase from Halothermothrix orenii Reveals Its Mechanism of Action and Binding Mode Authors: Chua, T.K. / Bujnicki, J.M. / Tan, T.-C. / Huynh, F. / Patel, B.K. / Sivaraman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r66.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r66.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 2r66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r66_validation.pdf.gz | 785.1 KB | Display | wwPDB validaton report |
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Full document | 2r66_full_validation.pdf.gz | 798.1 KB | Display | |
Data in XML | 2r66_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 2r66_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/2r66 ftp://data.pdbj.org/pub/pdb/validation_reports/r6/2r66 | HTTPS FTP |
-Related structure data
Related structure data | 2r60SC 2r68C 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: 56882.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halothermothrix orenii (bacteria) / Strain: H 168 / Gene: SPS / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q2ADF5, UniProt: B8CZ51*PLUS, sucrose-phosphate synthase |
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#2: Sugar | ChemComp-F6P / |
#3: Water | ChemComp-HOH / |
Sequence details | THE FIRST THREE RESIDUES, MET 1, VAL 2, AND GLU 3 ARE PART OF THE GENE PRODUCT. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 4000, 0.6M NaCl, 0.1M Na MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 13, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 13734 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Χ2: 1.394 / Net I/σ(I): 14.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2R60 Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Bsol: 52.904 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.807 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Xplor file |
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