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- PDB-5jp0: Bacteroides ovatus Xyloglucan PUL GH3B with bound glucose -

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Basic information

Entry
Database: PDB / ID: 5jp0
TitleBacteroides ovatus Xyloglucan PUL GH3B with bound glucose
ComponentsBeta-glucosidase BoGH3B
KeywordsHYDROLASE / Glycoside hydrolase / GH3
Function / homology
Function and homology information


symbiotic process benefiting host / xyloglucan catabolic process / beta-glucosidase / beta-glucosidase activity / periplasmic space
Similarity search - Function
Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / : / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain ...Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / : / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Beta-glucosidase BoGH3B
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase BoGH3B
B: Beta-glucosidase BoGH3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,3766
Polymers172,9672
Non-polymers4094
Water8,323462
1
A: Beta-glucosidase BoGH3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6883
Polymers86,4831
Non-polymers2042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucosidase BoGH3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6883
Polymers86,4831
Non-polymers2042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.169, 104.068, 160.444
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 26 - 782 / Label seq-ID: 4 - 760

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Beta-glucosidase BoGH3B / Glycosyl hydrolase family protein 3B / BoGH3B


Mass: 86483.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_02659 / Plasmid: pET-21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7LXU3, beta-glucosidase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium acetate, 15-25% PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→47.57 Å / Num. obs: 72918 / % possible obs: 99.9 % / Redundancy: 8.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.151 / Net I/σ(I): 11.4
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.923 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ex1

1ex1


Resolution: 2.3→47.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 13.096 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.205 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21086 3561 4.9 %RANDOM
Rwork0.17697 ---
obs0.17863 69286 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.059 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---0.12 Å20 Å2
3----1.4 Å2
Refinement stepCycle: 1 / Resolution: 2.3→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11508 0 26 462 11996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911788
X-RAY DIFFRACTIONr_bond_other_d0.0040.0211012
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.95516025
X-RAY DIFFRACTIONr_angle_other_deg1.036325342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64151486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58624.971517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.511151931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9791551
X-RAY DIFFRACTIONr_chiral_restr0.080.21786
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113433
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022614
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_it2.8111.8735956
X-RAY DIFFRACTIONr_mcbond_other2.8111.8725955
X-RAY DIFFRACTIONr_mcangle_it3.6842.7967438
X-RAY DIFFRACTIONr_mcangle_other3.6832.7977439
X-RAY DIFFRACTIONr_scbond_it4.152.1315832
X-RAY DIFFRACTIONr_scbond_other4.1492.1315832
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4413.0838588
X-RAY DIFFRACTIONr_long_range_B_refined6.315.54313384
X-RAY DIFFRACTIONr_long_range_B_other6.30715.42913223
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 94580 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 234 -
Rwork0.25 5085 -
obs--99.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.98530.07180.39130.55680.00471.20610.0310.13790.0005-0.22870.0157-0.02190.16910.155-0.04660.26610.04410.03410.03430.00130.009860.38118.67933.98
20.7118-0.2127-0.62611.14950.69311.99710.021-0.0050.1673-0.14720.0381-0.1973-0.19580.3654-0.05910.183-0.01650.02290.11490.0260.095874.49836.13749.643
30.35640.14760.27591.15470.32741.21620.1002-0.0881-0.01520.1459-0.0273-0.08310.20360.0399-0.07290.18310.0244-0.00460.04370.00130.009464.63712.20383.113
40.7967-0.71150.72861.5903-0.60030.80910.0728-0.0831-0.09640.07020.02980.1320.2414-0.1265-0.10260.2969-0.05280.01510.0745-0.00020.048142.234-0.70768.542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 581
2X-RAY DIFFRACTION2A582 - 782
3X-RAY DIFFRACTION3B26 - 632
4X-RAY DIFFRACTION4B633 - 782

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