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- PDB-5joz: Bacteroides ovatus Xyloglucan PUL GH43B -

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Basic information

Entry
Database: PDB / ID: 5joz
TitleBacteroides ovatus Xyloglucan PUL GH43B
ComponentsNon-reducing end alpha-L-arabinofuranosidase BoGH43B
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
Non-reducing end alpha-L-arabinofuranosidase BoGH43B
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsHemsworth, G.R. / Thompson, A.J. / 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 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-reducing end alpha-L-arabinofuranosidase BoGH43B
B: Non-reducing end alpha-L-arabinofuranosidase BoGH43B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6904
Polymers114,6102
Non-polymers802
Water3,765209
1
A: Non-reducing end alpha-L-arabinofuranosidase BoGH43B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3452
Polymers57,3051
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-reducing end alpha-L-arabinofuranosidase BoGH43B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3452
Polymers57,3051
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.460, 71.400, 160.300
Angle α, β, γ (deg.)90.00, 94.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Non-reducing end alpha-L-arabinofuranosidase BoGH43B / Glycosyl hydrolase family protein 43B / BoGH43B


Mass: 57305.031 Da / Num. of mol.: 2 / Fragment: UNP residues 24-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_02656 / Plasmid: pET-21a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A7LXU0, non-reducing end alpha-L-arabinofuranosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M sodium acetate pH 5, 20-30% PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.28→52.19 Å / Num. obs: 46976 / % possible obs: 99.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.1
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yrz

1yrz


Resolution: 2.28→52.19 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.557 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25023 2358 5 %RANDOM
Rwork0.19222 ---
obs0.19513 44617 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.601 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20.83 Å2
2---3.41 Å20 Å2
3---1.87 Å2
Refinement stepCycle: 1 / Resolution: 2.28→52.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7723 0 2 209 7934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197963
X-RAY DIFFRACTIONr_bond_other_d0.0020.027101
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9310884
X-RAY DIFFRACTIONr_angle_other_deg0.911316311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7751009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.90523.711353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.198151098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6511538
X-RAY DIFFRACTIONr_chiral_restr0.0770.21167
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219217
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021925
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_it3.1713.4254042
X-RAY DIFFRACTIONr_mcbond_other3.1683.4244041
X-RAY DIFFRACTIONr_mcangle_it4.4745.135049
X-RAY DIFFRACTIONr_mcangle_other4.4735.135050
X-RAY DIFFRACTIONr_scbond_it3.5933.6183921
X-RAY DIFFRACTIONr_scbond_other3.5923.6183922
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0665.3165835
X-RAY DIFFRACTIONr_long_range_B_refined6.6227.3198462
X-RAY DIFFRACTIONr_long_range_B_other6.62127.3158433
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 164 -
Rwork0.276 3270 -
obs--99.51 %

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