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- PDB-6euf: The GH43, Beta 1,3 Galactosidase, BT0265 -

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Basic information

Entry
Database: PDB / ID: 6euf
TitleThe GH43, Beta 1,3 Galactosidase, BT0265
ComponentsBeta-glucanase
KeywordsHYDROLASE / Arabiogalactan / GH43 / Beta 1 / 3 galactosidase / Hexasaccharide
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Ricin B-like lectins / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsCartmell, A. / Gilbert, H.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council322820 United Kingdom
CitationJournal: Nat Microbiol / Year: 2018
Title: A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation.
Authors: Cartmell, A. / Munoz-Munoz, J. / Briggs, J.A. / Ndeh, D.A. / Lowe, E.C. / Basle, A. / Terrapon, N. / Stott, K. / Heunis, T. / Gray, J. / Yu, L. / Dupree, P. / Fernandes, P.Z. / Shah, S. / ...Authors: Cartmell, A. / Munoz-Munoz, J. / Briggs, J.A. / Ndeh, D.A. / Lowe, E.C. / Basle, A. / Terrapon, N. / Stott, K. / Heunis, T. / Gray, J. / Yu, L. / Dupree, P. / Fernandes, P.Z. / Shah, S. / Williams, S.J. / Labourel, A. / Trost, M. / Henrissat, B. / Gilbert, H.J.
History
DepositionOct 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2019Group: Data collection / Category: chem_comp / reflns_shell / Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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 2.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucanase
B: Beta-glucanase
C: Beta-glucanase
D: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,1088
Polymers218,6864
Non-polymers3,4234
Water9,692538
1
A: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4542
Polymers54,6711
Non-polymers7831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6002
Polymers54,6711
Non-polymers9291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6002
Polymers54,6711
Non-polymers9291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4542
Polymers54,6711
Non-polymers7831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.000, 119.700, 182.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Beta-glucanase


Mass: 54671.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_0265 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8AB46
#2: Polysaccharide alpha-L-arabinofuranose-(1-3)-[alpha-L-arabinofuranose-(1-4)][beta-D-glucopyranuronic acid-(1-6)] ...alpha-L-arabinofuranose-(1-3)-[alpha-L-arabinofuranose-(1-4)][beta-D-glucopyranuronic acid-(1-6)]beta-D-galactopyranose-(1-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 782.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-3[LArafa1-4][DGlcpAb1-6]DGalpb1-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2112h-1b_1-5][a211h-1a_1-4][a2122A-1b_1-5]/1-1-2-2-3/a6-b1_b3-c1_b4-d1_b6-e1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+1)][b-D-Galp]{[(3+1)][a-L-Araf]{}[(4+1)][a-L-Araf]{}[(6+1)][b-D-GlcpA]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-rhamnopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-6)-[alpha-L-arabinofuranose-(1-3)] ...alpha-L-rhamnopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-6)-[alpha-L-arabinofuranose-(1-3)][alpha-L-arabinofuranose-(1-4)]beta-D-galactopyranose-(1-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 928.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-4DGlcpAb1-6[LArafa1-3][LArafa1-4]DGalpb1-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2112h-1b_1-5][a211h-1a_1-4][a2122A-1b_1-5][a2211m-1a_1-5]/1-1-2-2-3-4/a6-b1_b3-c1_b4-d1_b6-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+1)][b-D-Galp]{[(3+1)][a-L-Araf]{}[(4+1)][a-L-Araf]{}[(6+1)][b-D-GlcpA]{[(4+1)][a-L-Rhap]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3350 0.2 M Sodium Thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.93 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.2→100.4 Å / Num. obs: 117960 / % possible obs: 100 % / Redundancy: 13.3 % / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 2.2→100.04 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.903 / SU B: 7.23 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.227 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27086 5837 5 %RANDOM
Rwork0.20822 ---
obs0.21135 112028 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.978 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-0 Å2
2--0.32 Å20 Å2
3---0.68 Å2
Refinement stepCycle: 1 / Resolution: 2.2→100.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14907 0 232 538 15677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215568
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213282
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.94821178
X-RAY DIFFRACTIONr_angle_other_deg1.042330834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.71451890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79924.462744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.568152378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1591564
X-RAY DIFFRACTIONr_chiral_restr0.1080.22281
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217436
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023364
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_it2.8083.7397557
X-RAY DIFFRACTIONr_mcbond_other2.8073.7397556
X-RAY DIFFRACTIONr_mcangle_it3.9745.5949442
X-RAY DIFFRACTIONr_mcangle_other3.9735.5959443
X-RAY DIFFRACTIONr_scbond_it3.0793.9498011
X-RAY DIFFRACTIONr_scbond_other3.0793.9498011
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3575.84211735
X-RAY DIFFRACTIONr_long_range_B_refined5.76541.18916311
X-RAY DIFFRACTIONr_long_range_B_other5.76641.18816311
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 393 -
Rwork0.275 8244 -
obs--100 %

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