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- PDB-6eon: Galactanase BT0290 -

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Basic information

Entry
Database: PDB / ID: 6eon
TitleGalactanase BT0290
ComponentsBeta-galactosidase
KeywordsHYDROLASE / arabinogalactan proteins / X-ray crystallography / glycoside hydrolases / galactosidases / human gut microbiota
Function / homology
Function and homology information


galactose catabolic process / vacuole / beta-galactosidase activity / metal ion binding
Similarity search - Function
: / Beta-galactosidase, first all-beta domain / : / Beta-galactosidase, galactose-binding domain / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain ...: / Beta-galactosidase, first all-beta domain / : / Beta-galactosidase, galactose-binding domain / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-D-galactopyranose / Beta-galactosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBasle, A. / Munoz, J. / Gilbert, H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome TrustWT097907AIA United Kingdom
European Research Council322820
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 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / 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 1.2Jul 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 1.3Jan 17, 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-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0133
Polymers88,7931
Non-polymers2202
Water11,259625
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint4 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.038, 101.162, 143.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Beta-galactosidase / Galactanase


Mass: 88792.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_0290 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8AB22
#2: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-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.: 625 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol (racemic), 20 mM 2-Propanol, 20 mM 1,4-Butanediol, 20 mM 1,3-Propanediol, 100 mM Imidazole-MES pH 6.5, 30% Glycerol and 30% polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→46.61 Å / Num. obs: 92027 / % possible obs: 99.3 % / Redundancy: 7 % / CC1/2: 0.998 / Net I/σ(I): 13.8
Reflection shellResolution: 1.75→1.77 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4185 / CC1/2: 0.92 / % possible all: 92

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Processing

Software
NameVersionClassification
GDAdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D3A

3d3a


Resolution: 1.75→46.61 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.814 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17846 4544 4.9 %RANDOM
Rwork0.15624 ---
obs0.15737 87417 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.784 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.08 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.75→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6069 0 13 625 6707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196344
X-RAY DIFFRACTIONr_bond_other_d0.0020.025772
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9488605
X-RAY DIFFRACTIONr_angle_other_deg0.92313467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4955783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2624.71310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.545151109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0941529
X-RAY DIFFRACTIONr_chiral_restr0.0910.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021320
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_it1.1171.623045
X-RAY DIFFRACTIONr_mcbond_other1.1161.623044
X-RAY DIFFRACTIONr_mcangle_it1.7852.4263812
X-RAY DIFFRACTIONr_mcangle_other1.7852.4263813
X-RAY DIFFRACTIONr_scbond_it1.7531.8193299
X-RAY DIFFRACTIONr_scbond_other1.7531.8193299
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8582.6364779
X-RAY DIFFRACTIONr_long_range_B_refined4.20618.7247094
X-RAY DIFFRACTIONr_long_range_B_other4.20618.7247094
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.745→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 324 -
Rwork0.282 6049 -
obs--94.43 %

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