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Yorodumi- PDB-4a34: Crystal structure of the fucose mutarotase in complex with L-fuco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a34 | ||||||
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Title | Crystal structure of the fucose mutarotase in complex with L-fucose from Streptococcus pneumoniae | ||||||
Components | RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN | ||||||
Keywords | ISOMERASE | ||||||
Function / homology | Function and homology information monosaccharide metabolic process / D-ribose pyranase / D-ribose pyranase activity / monosaccharide binding Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.5 Å | ||||||
Authors | Higgins, M.A. / Boraston, A.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Structure of the Fucose Mutarotase from Streptococcus Pneumoniae in Complex with L-Fucose Authors: Higgins, M.A. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a34.cif.gz | 544.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a34.ent.gz | 454 KB | Display | PDB format |
PDBx/mmJSON format | 4a34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a34_validation.pdf.gz | 618.5 KB | Display | wwPDB validaton report |
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Full document | 4a34_full_validation.pdf.gz | 660.2 KB | Display | |
Data in XML | 4a34_validation.xml.gz | 106.7 KB | Display | |
Data in CIF | 4a34_validation.cif.gz | 144 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/4a34 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/4a34 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16574.094 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q04I09, UniProt: A0A0H2ZNZ5*PLUS #2: Sugar | ChemComp-FUL / #3: Chemical | ChemComp-K / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.39 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: RIGAKU AREA DETECTOR / Details: OSMIC 'BLUE' |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 97486 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.09 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.5→19.97 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.884 / SU B: 13.176 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 1.081 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.226 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.97 Å
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Refine LS restraints |
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