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- PDB-1odu: CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA-FUCOSIDASE IN COMP... -

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Entry
Database: PDB / ID: 1odu
TitleCRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA-FUCOSIDASE IN COMPLEX WITH FUCOSE
ComponentsPUTATIVE ALPHA-L-FUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / ALPHA-L-FUCOSIDASE / PRODUCT COMPLEX / THERMOSTABLE
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome
Similarity search - Function
Alpha-L-fucosidase, metazoa-type / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Alpha-L-fucosidase, metazoa-type / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-L-fucopyranose / Alpha-L-fucosidase, putative
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSulzenbacher, G. / Bignon, C. / Bourne, Y. / Henrissat, B.
Citation
Journal: J.Biol.Chem. / Year: 2004
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. / Withers, S. / Henrissat, B. / Bourne, Y.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Identification of the Catalytic Nucleophile of the Family 29 Alpha -L-Fucosidase from Thermotoga Maritima Through Trapping of a Covalent Glycosyl-Enzyme Intermediate and Mutagenesis
Authors: Tarling, C. / He, S. / Sulzenbacher, G. / Bignon, C. / Bourne, Y. / Henrissat, B. / Withers, S.
History
DepositionMar 14, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE ALPHA-L-FUCOSIDASE
B: PUTATIVE ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8724
Polymers104,5442
Non-polymers3282
Water00
1
A: PUTATIVE ALPHA-L-FUCOSIDASE
B: PUTATIVE ALPHA-L-FUCOSIDASE
hetero molecules

A: PUTATIVE ALPHA-L-FUCOSIDASE
B: PUTATIVE ALPHA-L-FUCOSIDASE
hetero molecules

A: PUTATIVE ALPHA-L-FUCOSIDASE
B: PUTATIVE ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,61712
Polymers313,6326
Non-polymers9856
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)179.080, 179.080, 174.692
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.70016, -0.71398, -0.00014), (-0.7138, 0.69999, -0.02232), (0.01604, -0.01553, -0.99975)
Vector: 0.17581, 1.3543, 90.02791)
DetailsBETWEEN THE ISOLATED CHAINS AND THAT FOR THE CHAINSIN THE COMPLEX IS IN AVERAGE 2464 (+/- 52) ANGSTROM**2.

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Components

#1: Protein PUTATIVE ALPHA-L-FUCOSIDASE


Mass: 52272.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ORF TM0306 / Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9WYE2, alpha-L-fucosidase
#2: Sugar ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
Compound detailsALPHA-L-FUCOSIDASE BELONGS TO GLYCOSYL HYDROLASASE FAMILY 29. THE ENZYME PERFORMS CATALYSIS WITH ...ALPHA-L-FUCOSIDASE BELONGS TO GLYCOSYL HYDROLASASE FAMILY 29. THE ENZYME PERFORMS CATALYSIS WITH RETENTION OF CONFIGURATION AT THE ANOMERIC CARBON. THE COORDINATES GIVEN DEFINE THE STRUCTURE OF ALPHA-L- FUCOSIDASE IN COMPLEX WITH FUCOSE. FUCOSE HAS UNDERGONE MUTAROTATION AND IS PRESENT AS THE BETA-CONFORMER.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 54.8 %
Crystal growpH: 8
Details: 18% PEG600, 5% JEFFAMINE M-600, 100 MM TRIS-HCL PH 8.0, PROTEIN CONCENTRATION 5 MG/ML FUCOSE WAS INTRODUCED BY SHORT SOAKING OF A NATIVE
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15.0 mg/mlprotein1drop
218 %(w/v)PEG60001reservoir
3100 mMTris-HCl1reservoirpH8.0
45 %Jeffamine M-6001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 16, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→57.7 Å / Num. obs: 24598 / % possible obs: 98.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 100.81 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 6.8
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.6 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 57 Å / Redundancy: 3.9 % / Num. measured all: 99148 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 98.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE ALPHA-L-FUCOSIDASE, PDB ENTRY 1HL8

1hl8


Resolution: 2.8→19.76 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 14.034 / SU ML: 0.274 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOLVENT NO WATER MOLECULES HAVE BEEN ADDED GIVEN THE MODEST RESOLUTION AND THE HIGH OVERALL DISORDER OF THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1848 7.1 %RANDOM
Rwork0.201 ---
obs0.203 24054 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.32 Å2-1.16 Å20 Å2
2---2.33 Å20 Å2
3---3.49 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7004 0 22 0 7026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0217252
X-RAY DIFFRACTIONr_bond_other_d0.0050.026321
X-RAY DIFFRACTIONr_angle_refined_deg0.9871.9399847
X-RAY DIFFRACTIONr_angle_other_deg0.757314708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9685839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027990
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021616
X-RAY DIFFRACTIONr_nbd_refined0.170.21381
X-RAY DIFFRACTIONr_nbd_other0.2120.26925
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.23969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2119
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0910.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.2112
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3041.54193
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.57326759
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.56733059
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.9894.53088
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 128
Rwork0.31 1762
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.72560.02430.04221.37890.11191.40.0541-0.21560.1680.0798-0.01890.0394-0.2025-0.2155-0.03510.12160.04420.03940.1839-0.01590.0182-22.503414.958465.4293
28.64390.688-0.3173.5264-1.4224.7107-0.04860.73970.4959-0.5520.42770.3204-0.0453-0.6754-0.37910.29830.1950.00140.48270.21760.4057-52.157825.092646.0867
32.31610.22680.08361.9157-0.13541.2896-0.06990.17470.6541-0.06240.05760.0001-0.214-0.02160.01220.1157-0.01110.00890.08540.07480.13955.174926.537223.9128
42.8802-0.4116-0.16881.5464-0.63935.736-0.0566-0.57130.80540.74060.1481-0.0357-0.54060.3907-0.09150.6402-0.0158-0.14290.2486-0.34781.183418.730955.216142.8062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 360
2X-RAY DIFFRACTION2A361 - 447
3X-RAY DIFFRACTION3B7 - 360
4X-RAY DIFFRACTION4B361 - 447
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.2011
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg0.99

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