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- PDB-4jfu: Crystal structure of a bacterial fucosidase with iminosugar inhibitor -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jfu | ||||||
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Title | Crystal structure of a bacterial fucosidase with iminosugar inhibitor | ||||||
![]() | alpha-L-fucosidase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / alpha-L-fucosidase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wright, D.W. / Davies, G.J. | ||||||
![]() | ![]() Title: alpha-L-fucosidase inhibition by pyrrolidine-ferrocene hybrids: rationalization of ligand-binding properties by structural studies. Authors: Hottin, A. / Wright, D.W. / Steenackers, A. / Delannoy, P. / Dubar, F. / Biot, C. / Davies, G.J. / Behr, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.4 KB | Display | ![]() |
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PDB format | ![]() | 170.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4jfsC ![]() 4jftC ![]() 4jfvC ![]() 4jfwC ![]() 4j27S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 52080.930 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-484 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: VPI-5482 / Plasmid: pET-YSBLIC / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 1113 molecules ![](data/chem/img/K80.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-IMD / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.26 % |
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Crystal grow | Temperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.16 M ammonium sulfate, 20% PEG 6K, 0.1M imidazole pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.659→55.385 Å / Num. all: 145075 / Num. obs: 145075 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.047 / Net I/σ(I): 10.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4J27 Resolution: 1.66→55.385 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.1929 / WRfactor Rwork: 0.1629 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8775 / SU B: 1.638 / SU ML: 0.054 / SU R Cruickshank DPI: 0.073 / SU Rfree: 0.0741 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY. THE MOLECULAR REPLACEMENT WAS NOT USED, COORDINATES FROM 4J27 WERE CONVERTED INTO THE (ALMOST) ISOMORPHOUS ...Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY. THE MOLECULAR REPLACEMENT WAS NOT USED, COORDINATES FROM 4J27 WERE CONVERTED INTO THE (ALMOST) ISOMORPHOUS CELL OF 4JFU TO BUILD A STARTING MODEL DIRECTLY. THE RFREE FLAG FROM 4J27 WAS USED FOR THIS DATASET.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.72 Å2 / Biso mean: 26.2193 Å2 / Biso min: 14.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→55.385 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.702 Å / Total num. of bins used: 20
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