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- PDB-6e61: Bacteroides ovatus mixed-linkage glucan utilization locus (MLGUL)... -

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Basic information

Entry
Database: PDB / ID: 6.0E+61
TitleBacteroides ovatus mixed-linkage glucan utilization locus (MLGUL) SGBP-A in complex with mixed-linkage heptasaccharide
Componentsmixed-linkage glucan utilization locus (MLGUL) SGBP-B
KeywordsSUGAR BINDING PROTEIN / tetratricopeptide repeat / outer membrane protein / binding protein
Function / homologySusD-like 2 / Starch-binding associating with outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / SusD/RagB family nutrient-binding outer membrane lipoprotein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsTamura, K. / Gardill, B.R. / Brumer, H. / Van Petegem, F.
CitationJournal: Cell.Mol.Life Sci. / Year: 2019
Title: Surface glycan-binding proteins are essential for cereal beta-glucan utilization by the human gut symbiont Bacteroides ovatus.
Authors: Tamura, K. / Foley, M.H. / Gardill, B.R. / Dejean, G. / Schnizlein, M. / Bahr, C.M.E. / Louise Creagh, A. / van Petegem, F. / Koropatkin, N.M. / Brumer, H.
History
DepositionJul 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
B: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,8668
Polymers125,3872
Non-polymers2,4796
Water7,566420
1
A: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8713
Polymers62,6931
Non-polymers1,1772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9955
Polymers62,6931
Non-polymers1,3014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.826, 92.943, 155.253
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein mixed-linkage glucan utilization locus (MLGUL) SGBP-B / Bacteroides ovatus surface glycan binding protein A from the mixed-linkage glucan utilization locus


Mass: 62693.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153 / Gene: BACOVA_02743 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A7LY27
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-3DGlcpb1-4DGlcpb1-4DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a2122h-1b_1-5]/1-1-1-1-1-1-1/a3-b1_b4-c1_c4-d1_d3-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M magnesium chloride, 0.1M HEPES, 25% (w/v) PEG3350
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-3 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. obs: 43053 / % possible obs: 98.6 % / Redundancy: 6.49 % / CC1/2: 0.997 / Net I/σ(I): 14.61
Reflection shellResolution: 2.51→2.66 Å / Redundancy: 5.37 % / Mean I/σ(I) obs: 3.51 / Num. unique obs: 6405 / CC1/2: 0.887 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DK2

6dk2


Resolution: 2.51→39.65 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.541 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 2112 4.9 %RANDOM
Rwork0.1729 ---
obs0.1754 40942 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.68 Å2 / Biso mean: 28.427 Å2 / Biso min: 7.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--2.03 Å2-0 Å2
3----1.44 Å2
Refinement stepCycle: final / Resolution: 2.51→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8175 0 166 420 8761
Biso mean--32.13 25.41 -
Num. residues----1038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0148548
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177269
X-RAY DIFFRACTIONr_angle_refined_deg0.9581.68511644
X-RAY DIFFRACTIONr_angle_other_deg1.4011.66717013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07451036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16923.515458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.665151315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8811540
X-RAY DIFFRACTIONr_chiral_restr0.0470.21172
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029596
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021652
X-RAY DIFFRACTIONr_mcbond_it0.9992.9524150
X-RAY DIFFRACTIONr_mcbond_other0.9982.9514149
X-RAY DIFFRACTIONr_mcangle_it1.6974.4255184
LS refinement shellResolution: 2.511→2.576 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 124 -
Rwork0.256 2517 -
all-2641 -
obs--83.29 %

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