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- PDB-5jov: Bacteroides ovatus Xyloglucan PUL GH31 with bound 5FIdoF -

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Basic information

Entry
Database: PDB / ID: 5jov
TitleBacteroides ovatus Xyloglucan PUL GH31 with bound 5FIdoF
ComponentsAlpha-xylosidase BoGH31A
KeywordsHYDROLASE / Glycoside hydrolase / GH31
Function / homology
Function and homology information


alpha-D-xyloside xylohydrolase / alpha-D-xyloside xylohydrolase / symbiotic process benefiting host / xyloglucan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / plasma membrane
Similarity search - Function
: / Jelly Rolls - #380 / : / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / glycosyl hydrolase (family 31) / PA14/GLEYA domain / PA14 domain profile. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain ...: / Jelly Rolls - #380 / : / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / glycosyl hydrolase (family 31) / PA14/GLEYA domain / PA14 domain profile. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5-fluoro-alpha-L-idopyranose / NICKEL (II) ION / Alpha-xylosidase BoGH31A
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 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: Alpha-xylosidase BoGH31A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7449
Polymers109,9381
Non-polymers8058
Water26,4101466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint17 kcal/mol
Surface area33610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.906, 108.448, 144.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Alpha-xylosidase BoGH31A / Glycosyl hydrolase family protein 31A / BoGH31A


Mass: 109938.469 Da / Num. of mol.: 1 / Fragment: UNP residues 22-954
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_02646 / Plasmid: pET-YSBL3C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): TUNER(DE3) / Variant (production host): TUNER / References: UniProt: A7LXT0, alpha-D-xyloside xylohydrolase
#5: Sugar ChemComp-B9D / 5-fluoro-alpha-L-idopyranose / (2R,3R,4R,5S,6R)-6-fluoranyl-6-(hydroxymethyl)oxane-2,3,4,5-tetrol / 5-fluoro-alpha-L-idose / 5-fluoro-L-idose / 5-fluoro-idose


Type: L-saccharide, alpha linking / Mass: 198.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H11FO6

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Non-polymers , 4 types, 1473 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1466 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium thiocyanate, 14-20% (w/v) PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→48.28 Å / Num. obs: 193532 / % possible obs: 99.7 % / Redundancy: 7.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.2
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.6 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xvg

2xvg


Resolution: 1.5→48.28 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.976 / SU B: 2.297 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.051 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14702 9749 5 %RANDOM
Rwork0.10726 ---
obs0.10927 183662 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.212 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---1.12 Å20 Å2
3---1.21 Å2
Refinement stepCycle: 1 / Resolution: 1.5→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7658 0 48 1466 9172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.028176
X-RAY DIFFRACTIONr_bond_other_d0.0020.027431
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.93911117
X-RAY DIFFRACTIONr_angle_other_deg0.966317153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35351018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14323.961414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.961151336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6441545
X-RAY DIFFRACTIONr_chiral_restr0.1090.21123
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219397
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022028
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_it1.611.6433869
X-RAY DIFFRACTIONr_mcbond_other1.581.6423868
X-RAY DIFFRACTIONr_mcangle_it1.9712.4784852
X-RAY DIFFRACTIONr_mcangle_other1.9832.4784853
X-RAY DIFFRACTIONr_scbond_it2.641.9344303
X-RAY DIFFRACTIONr_scbond_other2.641.9344303
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1882.796231
X-RAY DIFFRACTIONr_long_range_B_refined5.81616.91610903
X-RAY DIFFRACTIONr_long_range_B_other4.22514.8579891
X-RAY DIFFRACTIONr_rigid_bond_restr2.326315604
X-RAY DIFFRACTIONr_sphericity_free45.6415379
X-RAY DIFFRACTIONr_sphericity_bonded11.644516432
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 711 -
Rwork0.238 12959 -
obs--95.91 %

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