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- PDB-5mqs: Sialidase BT_1020 -

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Basic information

Entry
Database: PDB / ID: 5mqs
TitleSialidase BT_1020
ComponentsBeta-L-arabinobiosidase
KeywordsHYDROLASE / sialidase / arabinofuranosidase / plant pectin
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / exo-alpha-sialidase / exo-alpha-sialidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / : / Sialidase-like, CBM domain / BT_1020-like, N-terminal beta propeller / Glycoside hydrolase family 65, C-terminal / Glycosyl hydrolase family 65, C-terminal domain / : / Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain / BNR repeat-like domain / Sialidase ...: / : / Sialidase-like, CBM domain / BT_1020-like, N-terminal beta propeller / Glycoside hydrolase family 65, C-terminal / Glycosyl hydrolase family 65, C-terminal domain / : / Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain / BNR repeat-like domain / Sialidase / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Sialidase superfamily
Similarity search - Domain/homology
alpha-L-arabinofuranose / Exo-alpha-sialidase / Six-hairpin glycosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBasle, A. / Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Venditto, I. / Labourel, A. / Gilbert, H.J.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
iotechnology and Biological Research CouncilBB/K020358/1 United Kingdom
iotechnology and Biological Research CouncilBB/K001949/1 United Kingdom
Wellcome TrustWT097907MA United Kingdom
European Research Council322820 United Kingdom
CitationJournal: Nature / Year: 2017
Title: Complex pectin metabolism by gut bacteria reveals novel catalytic functions.
Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / ...Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / Field, R.A. / Zhu, Y. / O'Neill, M.A. / Urbanowicz, B.R. / York, W.S. / Davies, G.J. / Abbott, D.W. / Ralet, M.C. / Martens, E.C. / Henrissat, B. / Gilbert, H.J.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Aug 23, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _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_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: 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 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-L-arabinobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,7474
Polymers127,5341
Non-polymers2133
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-23 kcal/mol
Surface area39120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.433, 318.194, 90.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Beta-L-arabinobiosidase / BT_1020


Mass: 127533.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: hypBA2, Btheta7330_02635 / Plasmid: pet28b / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0P0FQG4, UniProt: Q8A8Z7*PLUS, (Ara-f)3-Hyp beta-L-arabinobiosidase
#2: Sugar ChemComp-AHR / alpha-L-arabinofuranose / alpha-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArafaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinofuranoseCOMMON NAMEGMML 1.0
a-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 3.57 Å3/Da / Density % sol: 65.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 15% (v/v) ethylene glycol, 15% (w/v) PEG 8000, 20 mM D-glucose, 20 mM D-mannose, 20 mM D- galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine, 300 mM L-arabinose, 44.5 mM imidazole, 55.5 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3→49.29 Å / Num. all: 274267 / Num. obs: 37085 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 7.4 % / CC1/2: 0.966 / Rmerge(I) obs: 0.312 / Net I/σ(I): 6.1
Reflection shellResolution: 3→3.13 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.316 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4450 / CC1/2: 0.632 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMAC5.8.0155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BT_1020 native

Resolution: 3→49.29 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.85 / SU B: 39.866 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.4 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26173 1950 5.3 %RANDOM
Rwork0.20724 ---
obs0.21004 35120 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.598 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å2-0 Å20 Å2
2--1.43 Å2-0 Å2
3----2.15 Å2
Refinement stepCycle: 1 / Resolution: 3→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8784 0 12 10 8806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199043
X-RAY DIFFRACTIONr_bond_other_d0.0020.028219
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.93912260
X-RAY DIFFRACTIONr_angle_other_deg0.956318928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1551081
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65423.866463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.698151487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3871560
X-RAY DIFFRACTIONr_chiral_restr0.0840.21242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110330
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022214
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_it0.3791.9754327
X-RAY DIFFRACTIONr_mcbond_other0.3791.9754326
X-RAY DIFFRACTIONr_mcangle_it0.6772.9625407
X-RAY DIFFRACTIONr_mcangle_other0.6772.9625408
X-RAY DIFFRACTIONr_scbond_it0.361.9894716
X-RAY DIFFRACTIONr_scbond_other0.361.9894716
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6462.976854
X-RAY DIFFRACTIONr_long_range_B_refined1.19421.99910037
X-RAY DIFFRACTIONr_long_range_B_other1.19422.00110038
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 137 -
Rwork0.416 2546 -
obs--99.93 %
Refinement TLS params.Method: refined / Origin x: -58.5896 Å / Origin y: -49.6445 Å / Origin z: 2.9642 Å
111213212223313233
T0.0419 Å2-0.0033 Å20.0232 Å2-0.0084 Å20.005 Å2--0.0671 Å2
L0.4137 °2-0.2103 °20.0477 °2-0.7292 °2-0.1094 °2--0.1947 °2
S0.0157 Å °0.047 Å °0.0929 Å °-0.0819 Å °-0.0072 Å °0.0118 Å °-0.038 Å °-0.0074 Å °-0.0085 Å °

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