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- PDB-6euh: The GH43, Beta 1,3 Galactosidase, BT3683 with galactodeoxynojirimycin -

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Basic information

Entry
Database: PDB / ID: 6euh
TitleThe GH43, Beta 1,3 Galactosidase, BT3683 with galactodeoxynojirimycin
ComponentsBeta-glucanaseGlucanase
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
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
Chem-DGJ / Beta-glucanase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 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: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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
B: Beta-glucanase
C: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4548
Polymers128,0083
Non-polymers4475
Water11,133618
1
A: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8723
Polymers42,6691
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8723
Polymers42,6691
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7092
Polymers42,6691
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.180, 77.200, 78.690
Angle α, β, γ (deg.)114.00, 101.78, 100.78
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta-glucanase / Glucanase


Mass: 42669.242 Da / Num. of mol.: 3
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: Chemical ChemComp-DGJ / (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol / 1-deoxygalactonojirimycin / Migalastat


Mass: 163.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13NO4 / Comment: medication, Galafold*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
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 PILATUS3 6M / 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: 99.9 % / Redundancy: 5.5 % / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2→68.19 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.722 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22559 3507 5.2 %RANDOM
Rwork0.18303 ---
obs0.18526 64330 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.755 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å2-0.18 Å20.01 Å2
2--0.19 Å20.09 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 2→68.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8208 0 25 618 8851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198535
X-RAY DIFFRACTIONr_bond_other_d0.0020.027504
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.93111593
X-RAY DIFFRACTIONr_angle_other_deg0.962317390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36751042
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50223.443395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.671151320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0261545
X-RAY DIFFRACTIONr_chiral_restr0.0920.21158
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219598
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021927
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_it1.5262.2584147
X-RAY DIFFRACTIONr_mcbond_other1.5262.2574146
X-RAY DIFFRACTIONr_mcangle_it2.3053.3765181
X-RAY DIFFRACTIONr_mcangle_other2.3053.3775182
X-RAY DIFFRACTIONr_scbond_it2.0572.5144388
X-RAY DIFFRACTIONr_scbond_other2.0572.5144389
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2653.6656408
X-RAY DIFFRACTIONr_long_range_B_refined4.78526.059647
X-RAY DIFFRACTIONr_long_range_B_other4.78526.0459646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 282 -
Rwork0.245 4620 -
obs--93.8 %

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