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- PDB-2wsp: Thermotoga maritima alpha-L-fucosynthase, TmD224G, in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2wsp
TitleThermotoga maritima alpha-L-fucosynthase, TmD224G, in complex with alpha-L-Fuc-(1-2)-beta-L-Fuc-N3
ComponentsALPHA-L-FUCOSIDASE, PUTATIVE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / CARBOHYDRATE SYNTHESIS / THERMOPHILIC ENZYME
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
Alpha-L-fucosidase, putative
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSulzenbacher, G. / Lipski, A. / Cobucci-Ponzano, B. / Conte, F. / Bedini, E. / Corsaro, M.M. / Parrilli, M. / Dal Piaz, F. / Lepore, L. / Rossi, M. / Moracci, M.
CitationJournal: Chem.Biol. / Year: 2009
Title: Beta-Glycosyl Azides as Substrates for Alpha-Glycosynthases: Preparation of Novel Efficient Alpha-L-Fucosynthases
Authors: Cobucci-Ponzano, B. / Conte, F. / Bedini, E. / Corsaro, M.M. / Parrilli, M. / Sulzenbacher, G. / Lipski, A. / Dal Piaz, F. / Lepore, L. / Rossi, M. / Moracci, M.
History
DepositionSep 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,1014
Polymers104,4282
Non-polymers6732
Water1,856103
1
A: ALPHA-L-FUCOSIDASE, PUTATIVE
hetero molecules

A: ALPHA-L-FUCOSIDASE, PUTATIVE
hetero molecules

A: ALPHA-L-FUCOSIDASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,6516
Polymers156,6423
Non-polymers1,0093
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area4010 Å2
ΔGint-17.9 kcal/mol
Surface area51410 Å2
MethodPISA
2
B: ALPHA-L-FUCOSIDASE, PUTATIVE
hetero molecules

B: ALPHA-L-FUCOSIDASE, PUTATIVE
hetero molecules

B: ALPHA-L-FUCOSIDASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,6516
Polymers156,6423
Non-polymers1,0093
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area4040 Å2
ΔGint-16.49 kcal/mol
Surface area50550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.249, 180.249, 169.733
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: (-0.21795, -0.97595, 0.00483), (-0.97589, 0.21787, -0.01263), (0.01128, -0.00747, -0.99991)
Vector: -0.50002, 0.68324, 85.45492)

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Components

#1: Protein ALPHA-L-FUCOSIDASE, PUTATIVE / ALPHA-L-FUCOSYNTHASE


Mass: 52214.012 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
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: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-L-fucosyl-azide


Type: oligosaccharide / Mass: 336.318 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a1221m-1b_1-5_1*N=^ZN=N][a1221m-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][<N2>]{[(1+1)][b-L-Fucp1N]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 224 TO GLY ENGINEERED RESIDUE IN CHAIN B, ASP 224 TO GLY
Sequence detailsD224G MUNTANT

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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: 2.58 Å3/Da / Density % sol: 52.29 % / Description: NONE
Crystal growDetails: 18 % PEG600, 5 % JEFFAMINE M-600, 100 MM TRIS-HCL PH 8.0, 14 MG/ML BETA-L-FUC-N3 PROTEIN CONC. 5 MG/ML

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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: Oct 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.65→35 Å / Num. obs: 30789 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 64.184 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.5
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HL8

1hl8


Resolution: 2.65→114.9 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 25.233 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GLOBAL B-FACTORS, CONTAINING RESIDUAL AND TLS COMPONENT HAVE BEEN DEPOSITED.
RfactorNum. reflection% reflectionSelection details
Rfree0.24059 1536 5.1 %RANDOM
Rwork0.20139 ---
obs0.20338 28873 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.774 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0.88 Å2-0 Å2
2---1.76 Å20 Å2
3---2.64 Å2
Refinement stepCycle: LAST / Resolution: 2.65→114.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 46 103 7317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227451
X-RAY DIFFRACTIONr_bond_other_d0.0010.025159
X-RAY DIFFRACTIONr_angle_refined_deg0.9491.95210123
X-RAY DIFFRACTIONr_angle_other_deg0.766312465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.335863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74323.389360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.158151210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.31542
X-RAY DIFFRACTIONr_chiral_restr0.0570.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218187
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021643
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3051.54308
X-RAY DIFFRACTIONr_mcbond_other0.0331.51767
X-RAY DIFFRACTIONr_mcangle_it0.58126947
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.67833143
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2124.53176
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: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 114 -
Rwork0.295 2086 -
obs--98.83 %
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)
10.82510.0234-0.49931.2727-0.12230.36330.02820.0846-0.1136-0.0502-0.1215-0.0769-0.07290.01560.09330.1205-0.0101-0.00550.13240.00590.13284.9546-26.30963.4392
24.7747-0.76730.81155.79881.10015.60960.22581.0038-0.923-0.8698-0.2114-0.22040.14310.1966-0.01440.15330.05650.07230.2118-0.19380.752618.9695-54.24743.595
30.9699-0.3334-0.35920.717-0.32720.903-0.01620.022-0.04760.0627-0.05310.0340.09070.06170.06930.15560.04410.01070.1950.00650.067924.4251-10.80822.2854
47.3538-1.41950.70553.1157-0.05527.6497-0.213-0.1398-0.13850.74650.1012-0.39810.73191.10380.11180.36210.2615-0.04560.3280.09340.350248.3492-29.891642.3058
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 357
2X-RAY DIFFRACTION2A358 - 447
3X-RAY DIFFRACTION3B5 - 357
4X-RAY DIFFRACTION4B358 - 447

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