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- PDB-6eui: The GH43, Beta 1,3 Galactosidase, BT3683 with galactose -

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Basic information

Entry
Database: PDB / ID: 6eui
TitleThe GH43, Beta 1,3 Galactosidase, BT3683 with galactose
ComponentsBeta-glucanase
KeywordsHYDROLASE / Arabiogalactan / GH43 / Beta 1 / 3 galactosidase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycosyl hydrolases family 16 / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Beta-glucanase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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: reflns_shell
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0704
Polymers42,6691
Non-polymers4003
Water4,828268
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-6 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.380, 136.380, 53.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Beta-glucanase


Mass: 42669.242 Da / Num. of mol.: 1
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_3683 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A1H8
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350 0.2 M Ammonium Formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.76→68.19 Å / Num. obs: 36549 / % possible obs: 99.5 % / Redundancy: 5.4 % / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BT0265

Resolution: 1.76→68.19 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.122 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.113 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21231 1860 5.1 %RANDOM
Rwork0.16803 ---
obs0.17021 34685 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.166 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å2-0 Å2
2--0.3 Å20 Å2
3----0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.76→68.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 25 268 3047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192889
X-RAY DIFFRACTIONr_bond_other_d0.0020.022540
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9383927
X-RAY DIFFRACTIONr_angle_other_deg0.95835906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4685354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20623.63135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19815456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9251515
X-RAY DIFFRACTIONr_chiral_restr0.0990.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02644
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_it1.9032.8721389
X-RAY DIFFRACTIONr_mcbond_other1.9022.8711388
X-RAY DIFFRACTIONr_mcangle_it2.6144.2981737
X-RAY DIFFRACTIONr_mcangle_other2.6154.31738
X-RAY DIFFRACTIONr_scbond_it2.6313.1461500
X-RAY DIFFRACTIONr_scbond_other2.6313.1461500
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0164.5982186
X-RAY DIFFRACTIONr_long_range_B_refined5.3732.8163243
X-RAY DIFFRACTIONr_long_range_B_other5.37232.8033240
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 141 -
Rwork0.309 2558 -
obs--99.89 %

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