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Open data
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Basic information
Entry | Database: PDB / ID: 1hl8 | ||||||
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Title | CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA-FUCOSIDASE | ||||||
![]() | PUTATIVE ALPHA-L-FUCOSIDASE | ||||||
![]() | HYDROLASE / GLYCOSIDE HYDROLASE / ALPHA-L-FUCOSIDASE / THERMOSTABLE | ||||||
Function / homology | ![]() alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sulzenbacher, G. / Bignon, C. / Bourne, Y. / Henrissat, B. | ||||||
![]() | ![]() Title: Crystal Structure of Thermotoga Maritima Alpha-L-Fucosidase. Insights Into the Catalytic Mechanism and the Molecular Basis for Fucosidosis. Authors: Sulzenbacher, G. / Bignon, C. / Nishimura, T. / Tarling, C.A. / Withers, S.G. / Henrissat, B. / Bourne, Y. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.5 KB | Display | ![]() |
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PDB format | ![]() | 152.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.2 KB | Display | ![]() |
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Full document | ![]() | 456 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 44.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.68906, -0.72382, -0.03587), Vector: |
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Components
#1: Protein | Mass: 52315.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ORF TM0306 / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Compound details | ALPHA-L-FUCOSIDASE BELONGS TO GLYCOSYL HYDROLASASE FAMILY 29. THE ENZYME PERFORMS CATALYSIS WITH ...ALPHA-L-FUCOSIDASE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.6 % Description: THE STRUCTURE WAS SOLVED BY MAD, BUT REFINED AGAINST NATIVE DATA ONLY | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: 18 % PEG600, 5 % JEFFAMINE, M-600 100 MM TRIS-HCL PH 8.0, PROTEIN CONC. 5 MG/ML | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 3, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→37.3 Å / Num. obs: 36833 / % possible obs: 99.1 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.8 / % possible all: 99.1 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 37 Å / % possible obs: 99.3 % / Redundancy: 5.7 % / Num. measured all: 212598 / Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS % possible obs: 99.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.8 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS RESIDUES SER 14 A, ARG 16 A, LYS 138 A, ARG 378 A, SER 14 B AND ARG 16 A ARE PRESENT IN DOUBLE DOUBLE CONFORMATION
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→37.27 Å
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Refine LS restraints |
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