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- PDB-5joy: Bacteroides ovatus Xyloglucan PUL GH43A in complex with AraLOG -

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Basic information

Entry
Database: PDB / ID: 5joy
TitleBacteroides ovatus Xyloglucan PUL GH43A in complex with AraLOG
ComponentsNon-reducing end alpha-L-arabinofuranosidase BoGH43A
KeywordsHYDROLASE / Glycoside hydrolase / GH43
Function / homology
Function and homology information


symbiotic process benefiting host / xyloglucan catabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / periplasmic space
Similarity search - Function
: / Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 ...: / Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
(Z)-L-Arabinonhydroximo-1,4-lactone / Non-reducing end alpha-L-arabinofuranosidase BoGH43A
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsThompson, A.J. / Hemsworth, G.R. / Stepper, J. / Sobala, L.F. / Coyle, T. / Larsbrink, J. / Spadiut, O. / Stubbs, K.A. / Brumer, H. / Davies, G.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K00591X/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/I014802/1 United Kingdom
European Research Council322942 United Kingdom
CitationJournal: Open Biology / Year: 2016
Title: Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut.
Authors: Hemsworth, G.R. / Thompson, A.J. / Stepper, J. / Sobala, F. / Coyle, T. / Larsbrink, J. / Spadiut, O. / Goddard-Borger, E.D. / Stubbs, K.A. / Brumer, H. / Davies, G.J.
History
DepositionMay 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / 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 1.3May 1, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-reducing end alpha-L-arabinofuranosidase BoGH43A
B: Non-reducing end alpha-L-arabinofuranosidase BoGH43A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7087
Polymers116,0762
Non-polymers6335
Water17,943996
1
A: Non-reducing end alpha-L-arabinofuranosidase BoGH43A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3854
Polymers58,0381
Non-polymers3473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-reducing end alpha-L-arabinofuranosidase BoGH43A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3233
Polymers58,0381
Non-polymers2852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.591, 91.505, 154.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-954-

HOH

21B-1134-

HOH

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Components

#1: Protein Non-reducing end alpha-L-arabinofuranosidase BoGH43A / Glycosyl hydrolase family protein 43A / BoGH43A


Mass: 58037.914 Da / Num. of mol.: 2 / Fragment: UNP residues 21-526
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_02654 / Plasmid: pET-YSBLLIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER
References: UniProt: A7LXT8, non-reducing end alpha-L-arabinofuranosidase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Sugar ChemComp-6LW / (Z)-L-Arabinonhydroximo-1,4-lactone / (2~{Z},3~{R},4~{R},5~{S})-2-hydroxyimino-5-(hydroxymethyl)oxolane-3,4-diol


Type: L-saccharide / Mass: 163.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H9NO5
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 996 / 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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M Tris pH 7.2 - 7.8, 0.18 M magnesium chloride and 12% (w/v) PEG-6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→46.49 Å / Num. obs: 84685 / % possible obs: 99.8 % / Redundancy: 7.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.44 / Mean I/σ(I) obs: 1.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GH43B to be deposited

Resolution: 1.9→46.49 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.171 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.142 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21796 4271 5 %RANDOM
Rwork0.17877 ---
obs0.18073 80337 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.966 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.9→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7837 0 42 996 8875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198356
X-RAY DIFFRACTIONr_bond_other_d0.0020.027549
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.94411437
X-RAY DIFFRACTIONr_angle_other_deg0.922317434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8951083
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76823.828384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.735151272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1471541
X-RAY DIFFRACTIONr_chiral_restr0.0840.21216
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219650
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022007
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_it1.1682.3334114
X-RAY DIFFRACTIONr_mcbond_other1.1682.3324109
X-RAY DIFFRACTIONr_mcangle_it1.8923.4945156
X-RAY DIFFRACTIONr_mcangle_other1.8923.4945157
X-RAY DIFFRACTIONr_scbond_it1.2952.4224242
X-RAY DIFFRACTIONr_scbond_other1.2952.4224242
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1063.5856245
X-RAY DIFFRACTIONr_long_range_B_refined4.93719.6810051
X-RAY DIFFRACTIONr_long_range_B_other4.93719.68210052
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 305 -
Rwork0.317 5862 -
obs--99.31 %

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