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- PDB-5xb7: GH42 alpha-L-arabinopyranosidase from Bifidobacterium animalis su... -

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Basic information

Entry
Database: PDB / ID: 5xb7
TitleGH42 alpha-L-arabinopyranosidase from Bifidobacterium animalis subsp. lactis Bl-04
ComponentsBeta-galactosidase
KeywordsHYDROLASE / alpha-l-arabinopyranosidase / GH42 / arabinopyranoside
Function / homology
Function and homology information


beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / beta-galactosidase
Similarity search - Component
Biological speciesBifidobacterium animalis subsp. lactis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsViborg, A.H. / Katayama, T. / Arakawa, T. / Abou Hachem, M. / Lo Leggio, L. / Kitaoka, M. / Svensson, B. / Fushinobu, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society of the Promotion of ScienceP15091 Japan
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Discovery of alpha-l-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 42.
Authors: Viborg, A.H. / Katayama, T. / Arakawa, T. / Abou Hachem, M. / Lo Leggio, L. / Kitaoka, M. / Svensson, B. / Fushinobu, S.
History
DepositionMar 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
E: Beta-galactosidase
F: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)484,23577
Polymers477,6336
Non-polymers6,60271
Water45,5422528
1
A: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,60333
Polymers238,8173
Non-polymers2,78730
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21040 Å2
ΔGint-135 kcal/mol
Surface area63080 Å2
MethodPISA
2
B: Beta-galactosidase
E: Beta-galactosidase
F: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,63244
Polymers238,8173
Non-polymers3,81641
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22640 Å2
ΔGint-166 kcal/mol
Surface area64700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.954, 177.954, 375.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Beta-galactosidase


Mass: 79605.531 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium animalis subsp. lactis (bacteria)
Strain: Bl-04 / Gene: AL0646_0018 / Plasmid: pET21a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1M2TTS0, UniProt: A0A2H4A2Z3*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2528 / 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: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% glycerol, 1.6 M ammonium sulfate, 0.1 M MES buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2014
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 400874 / % possible obs: 100 % / Redundancy: 14.9 % / Rsym value: 0.127 / Net I/σ(I): 27.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 19842 / CC1/2: 0.989 / Rsym value: 0.502 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KWG

1kwg


Resolution: 2→49.368 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19127 20004 5 %RANDOM
Rwork0.15525 ---
obs0.15704 380693 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å2-0 Å2
3---0.73 Å2
Refinement stepCycle: 1 / Resolution: 2→49.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32478 0 410 2528 35416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.01933740
X-RAY DIFFRACTIONr_bond_other_d00.0230501
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.93345965
X-RAY DIFFRACTIONr_angle_other_deg3.704369841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78954108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46523.4211666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.277154897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.77215233
X-RAY DIFFRACTIONr_chiral_restr0.1290.24957
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02138683
X-RAY DIFFRACTIONr_gen_planes_other0.0230.028338
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_it2.3442.51716465
X-RAY DIFFRACTIONr_mcbond_other2.3442.51716464
X-RAY DIFFRACTIONr_mcangle_it2.8743.75920562
X-RAY DIFFRACTIONr_mcangle_other2.8743.7620563
X-RAY DIFFRACTIONr_scbond_it3.3382.7817275
X-RAY DIFFRACTIONr_scbond_other3.3312.77717259
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6344.05525380
X-RAY DIFFRACTIONr_long_range_B_refined5.76121.1841882
X-RAY DIFFRACTIONr_long_range_B_other5.76121.1841883
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 1523 -
Rwork0.188 27766 -
obs--99.63 %

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