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- PDB-6or4: Crystal structure of SpGH29 -

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Basic information

Entry
Database: PDB / ID: 6or4
TitleCrystal structure of SpGH29
ComponentsGlycoside hydrolase
KeywordsHYDROLASE / glycoside hydrolase
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome / metal ion binding
Similarity search - Function
CalX-like domain superfamily / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Coagulation factors 5/8 type C domain (FA58C) profile. / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Lewis A antigen, beta anomer / F5/8 type C domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsPluvinage, B. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Two complementary alpha-fucosidases fromStreptococcus pneumoniaepromote complete degradation of host-derived carbohydrate antigens.
Authors: Hobbs, J.K. / Pluvinage, B. / Robb, M. / Smith, S.P. / Boraston, A.B.
History
DepositionApr 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 4, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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 2.1Aug 5, 2020Group: Derived calculations / Structure summary / Category: pdbx_molecule_features / struct_conn / Item: _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 11, 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: Glycoside hydrolase
B: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9834
Polymers101,9242
Non-polymers1,0592
Water11,962664
1
A: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4912
Polymers50,9621
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4912
Polymers50,9621
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.960, 68.820, 72.670
Angle α, β, γ (deg.)76.580, 73.240, 73.610
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glycoside hydrolase / SPGH29


Mass: 50961.961 Da / Num. of mol.: 2 / Mutation: D171N, E215Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_2146 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2US78
#2: Polysaccharide beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis A antigen, beta anomer
DescriptorTypeProgram
DGalpb1-3[LFucpa1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20 % PEG 3350, 0.2 M NaCl, 1 mM DTT and 0.1 M Tris.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→46.59 Å / Num. obs: 50203 / % possible obs: 98 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.062 / Net I/σ(I): 14.1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4093 / CC1/2: 0.895 / Rpim(I) all: 0.344 / % possible all: 96.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EYP

3eyp


Resolution: 2.1→46.59 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.264 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 2494 5 %RANDOM
Rwork0.1689 ---
obs0.1721 47708 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.28 Å2 / Biso mean: 22.781 Å2 / Biso min: 8.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å22.24 Å21.52 Å2
2--1.2 Å2-0.71 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.1→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7132 0 72 664 7868
Biso mean--31.6 27.19 -
Num. residues----898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0127461
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.64810169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4315906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40723.022407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.444151166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2321539
X-RAY DIFFRACTIONr_chiral_restr0.1030.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025846
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 171 -
Rwork0.251 3530 -
all-3701 -
obs--96.78 %

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