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Yorodumi- PDB-2r60: Structure of apo Sucrose Phosphate Synthase (SPS) of Halothermoth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r60 | ||||||
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Title | Structure of apo Sucrose Phosphate Synthase (SPS) 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 / SYNCHROTRON / Resolution: 1.8 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 | 2r60.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r60.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 2r60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r60_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
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Full document | 2r60_full_validation.pdf.gz | 445.6 KB | Display | |
Data in XML | 2r60_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 2r60_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/2r60 ftp://data.pdbj.org/pub/pdb/validation_reports/r6/2r60 | HTTPS FTP |
-Related 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) / Gene: SPS / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q2ADF5, UniProt: B2CCB8*PLUS, sucrose-phosphate synthase |
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#2: Water | ChemComp-HOH / |
Sequence details | (MET A 1), (VAL A 2), (GLU A 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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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9788 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 5, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 49698 / % possible obs: 97.2 % / Redundancy: 6.7 % / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.1 % / Num. unique all: 3851 / % possible all: 75.9 |
-Processing
Software |
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Refinement | Resolution: 1.8→20 Å / σ(F): 6152
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Solvent computation | Bsol: 69.321 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.322 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Xplor file |
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