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- PDB-5mqr: Sialidase BT_1020 -

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Basic information

Entry
Database: PDB / ID: 5mqr
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 / 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 / Neuraminidase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Exo-alpha-sialidase / Six-hairpin glycosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

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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)130,22610
Polymers129,2221
Non-polymers1,0049
Water16,033890
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-8 kcal/mol
Surface area39300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.720, 316.998, 90.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1543-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-L-arabinobiosidase / BT_1020


Mass: 129221.969 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

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Non-polymers , 6 types, 899 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 890 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 14% (v/v) ethylene glycol, 14% (w/v) PEG 8000, 30 mM of each di-, tri, tetra- and penta-ethylene glycol, 50 mM hepes and 50 mM MOPS pH 7.5

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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: 2.2→49.25 Å / Num. obs: 90935 / % possible obs: 99.3 % / Observed criterion σ(I): 1.5 / Redundancy: 6.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.145 / Net I/σ(I): 9.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.495 / % possible all: 97.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
SHELXDEphasing
Cootmodel building
REFMAC5.8.0155refinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→49.25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.739 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.147 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 4591 5 %RANDOM
Rwork0.1643 ---
obs0.16585 86325 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.308 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å2-0 Å2-0 Å2
2---0.89 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 2.2→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8784 0 61 890 9735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199100
X-RAY DIFFRACTIONr_bond_other_d0.0020.028290
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.95612328
X-RAY DIFFRACTIONr_angle_other_deg0.953319099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6695.0091086
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0223.892465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.604151384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7411560
X-RAY DIFFRACTIONr_chiral_restr0.0920.21246
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110359
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022217
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_it0.7592.0884331
X-RAY DIFFRACTIONr_mcbond_other0.7582.0874330
X-RAY DIFFRACTIONr_mcangle_it1.2853.1285413
X-RAY DIFFRACTIONr_mcangle_other1.2853.1295414
X-RAY DIFFRACTIONr_scbond_it1.0762.2324769
X-RAY DIFFRACTIONr_scbond_other1.0752.2324769
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7783.286915
X-RAY DIFFRACTIONr_long_range_B_refined3.84624.77910518
X-RAY DIFFRACTIONr_long_range_B_other3.84624.78510519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 346 -
Rwork0.272 6196 -
obs--98.2 %
Refinement TLS params.Method: refined / Origin x: 4.6761 Å / Origin y: 109.0239 Å / Origin z: 2.9134 Å
111213212223313233
T0.0293 Å2-0.004 Å20.0149 Å2-0.0146 Å2-0.005 Å2--0.0113 Å2
L0.3161 °2-0.187 °20.0431 °2-0.7777 °2-0.1498 °2--0.2535 °2
S0.0228 Å °0.0611 Å °-0.0043 Å °-0.0841 Å °-0.0053 Å °-0.0038 Å °0.0084 Å °0.0082 Å °-0.0175 Å °

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