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- PDB-4j27: 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: 4j27 | ||||||
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Title | Crystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroides thetaiotaomicron in a novel crystal form | ||||||
![]() | Alpha-L-fucosidase | ||||||
![]() | HYDROLASE / Alpha-L-fucosidase | ||||||
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 | ![]() | 214.9 KB | Display | ![]() |
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PDB format | ![]() | 167.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4j28C ![]() 2wvvS C: citing same article ( S: Starting model for refinement |
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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 - 471 / Label seq-ID: 1 - 437
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Components
#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: ![]() ![]() #2: Chemical | ChemComp-IMD / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.95 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 17% PEG 6K, 0.124M ammonium sulfate, 0.1M imidazole 2 parts protein: 3 mother liquor, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 21, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.59→30.666 Å / Num. all: 164706 / Num. obs: 164706 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.112 / Net I/σ(I): 8.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WVV Resolution: 1.59→30.666 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1694 / WRfactor Rwork: 0.1497 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8693 / SU B: 1.577 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0654 / SU Rfree: 0.0655 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.065 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.97 Å2 / Biso mean: 15.8145 Å2 / Biso min: 5.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→30.666 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 26913 / 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: 1.591→1.632 Å / Total num. of bins used: 20
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