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- PDB-6orf: Crystal structure of SpGH29 -

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Basic information

Entry
Database: PDB / ID: 6orf
TitleCrystal structure of SpGH29
ComponentsSpGH29
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 X antigen, alpha 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: 1.7 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 30, 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 / entity_name_com / 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_molecule_features / 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_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 2.1Oct 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

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Assembly

Deposited unit
A: SpGH29
B: SpGH29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,46910
Polymers102,0382
Non-polymers1,4318
Water19,2941071
1
A: SpGH29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8597
Polymers51,0191
Non-polymers8406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SpGH29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6113
Polymers51,0191
Non-polymers5922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.991, 98.982, 79.090
Angle α, β, γ (deg.)90.000, 97.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SpGH29


Mass: 51019.012 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 alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose / Lewis X antigen / alpha anomer


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 X antigen, alpha anomer
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1071 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21 % PEG 4000, 0.22 M NaOAc, 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: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.7→78.4 Å / Num. obs: 113304 / % possible obs: 96.7 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.035 / Net I/σ(I): 13.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 16592 / CC1/2: 0.919 / Rpim(I) all: 0.165 / % possible all: 97.1

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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: 1.7→49.54 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.997 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 5630 5 %RANDOM
Rwork0.1739 ---
obs0.1757 107649 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.02 Å2 / Biso mean: 18.514 Å2 / Biso min: 7.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å2-0.87 Å2
2--0.38 Å20 Å2
3---0.38 Å2
Refinement stepCycle: final / Resolution: 1.7→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7160 0 96 1071 8327
Biso mean--17.68 27.46 -
Num. residues----898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127591
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.64810327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2695924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15723.077416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.436151205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0041540
X-RAY DIFFRACTIONr_chiral_restr0.0990.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025952
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 440 -
Rwork0.21 8026 -
all-8466 -
obs--97.75 %

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