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- PDB-4j28: Crystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j28 | ||||||
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Title | Crystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroides thetaiotaomicron in complex with a 5-membered iminocyclitol 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. | ||||||
![]() | ![]() Title: Three dimensional structure of a bacterial alpha-l-fucosidase with a 5-membered iminocyclitol inhibitor. Authors: Wright, D.W. / Moreno-Vargas, A.J. / Carmona, A.T. / Robina, I. / Davies, G.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 207.2 KB | Display | ![]() |
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PDB format | ![]() | 161.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.7 KB | Display | ![]() |
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Full document | ![]() | 493.7 KB | Display | |
Data in XML | ![]() | 39.3 KB | Display | |
Data in CIF | ![]() | 59.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4j27SC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 35 - 472 / Label seq-ID: 1 - 438
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 52080.930 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 35-484 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: VPI-5482 / Plasmid: PET28 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 743 molecules ![](data/chem/img/EAT.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-IMD / #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.79 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10.45% PEG 6K, 0.12M ammonium sulfate, 0.095M imidazole, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-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: 1.73→29.013 Å / Num. all: 128218 / Num. obs: 128218 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.045 / Net I/σ(I): 12.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4J27 Resolution: 1.73→29.01 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1821 / WRfactor Rwork: 0.1593 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7446 / SU B: 3.238 / SU ML: 0.092 / SU R Cruickshank DPI: 0.0895 / SU Rfree: 0.0873 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. THE COORDINATES FROM 4J27 WERE CONVERTED INTO THE (ALMOST) ISOMORPHOUS CELL OF 4J28 TO BUILD A STARTING ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. THE COORDINATES FROM 4J27 WERE CONVERTED INTO THE (ALMOST) ISOMORPHOUS CELL OF 4J28 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: 106.9 Å2 / Biso mean: 34.2843 Å2 / Biso min: 20.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→29.01 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 26587 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.73→1.775 Å / Total num. of bins used: 20
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