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

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Basic information

Entry
Database: PDB / ID: 6dmf
TitleBacteroides ovatus mixed-linkage glucan utilization locus (MLGUL) SGBP-A with cellohexaose
Componentsmixed-linkage glucan utilization locus (MLGUL) SGBP-B
KeywordsSUGAR BINDING PROTEIN / SGBP-A / Bacteroides ovatus / SusD / beta-glucan
Function / homologySusD-like 2 / Starch-binding associating with outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / beta-cellopentaose / beta-cellohexaose / ACETATE ION / DI(HYDROXYETHYL)ETHER / SusD/RagB family nutrient-binding outer membrane lipoprotein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsKoropatkin, N.M. / Bahr, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118475 United States
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
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / 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_molecule_features / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.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
C: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
D: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
E: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
F: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
G: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
H: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
I: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
J: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)598,07862
Polymers585,90910
Non-polymers12,16952
Water17,006944
1
A: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7777
Polymers58,5911
Non-polymers1,1866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0028
Polymers58,5911
Non-polymers1,4117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8517
Polymers58,5911
Non-polymers1,2606
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7275
Polymers58,5911
Non-polymers1,1364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9138
Polymers58,5911
Non-polymers1,3227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6654
Polymers58,5911
Non-polymers1,0743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9168
Polymers58,5911
Non-polymers1,3267
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7275
Polymers58,5911
Non-polymers1,1364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7275
Polymers58,5911
Non-polymers1,1364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7715
Polymers58,5911
Non-polymers1,1804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)228.845, 228.845, 246.517
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
mixed-linkage glucan utilization locus (MLGUL) SGBP-B


Mass: 58590.934 Da / Num. of mol.: 10 / Fragment: UNP residues 40-558
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153) (bacteria)
Strain: ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153 / Gene: BACOVA_02743 / Production host: Escherichia coli (E. coli) / References: UniProt: A7LY27

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Sugars , 2 types, 10 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellopentaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellohexaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 990.860 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellohexaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 986 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 944 / 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: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Molecular Dimensions Crystal Strategy Screen I, well G3 (0.2 M magnesium chloride, 0.1 M Tris acetate, pH 8.5, 25% PEG2000 MME).
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→49.6 Å / Num. obs: 283596 / % possible obs: 99.93 % / Redundancy: 8.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.2249 / Rrim(I) all: 0.2396 / Net I/σ(I): 8.4
Reflection shellResolution: 2.4→2.487 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.755 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 28197 / CC1/2: 0.58 / % possible all: 99.52

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0222refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6DK2

6dk2


Resolution: 2.4→49.6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 22.491 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.235
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 14140 5 %RANDOM
Rwork0.1896 ---
obs0.1922 269456 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 147.66 Å2 / Biso mean: 34.414 Å2 / Biso min: 15.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å2-0.74 Å20 Å2
2---1.49 Å20 Å2
3---4.83 Å2
Refinement stepCycle: final / Resolution: 2.4→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40685 0 812 944 42441
Biso mean--50.96 48.51 -
Num. residues----5139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01442492
X-RAY DIFFRACTIONr_bond_other_d0.0010.01736281
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.68257804
X-RAY DIFFRACTIONr_angle_other_deg0.8121.66784972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32355119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69823.4992289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77156622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.64615200
X-RAY DIFFRACTIONr_chiral_restr0.0470.25773
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0247679
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028209
X-RAY DIFFRACTIONr_rigid_bond_restr3.612378499
X-RAY DIFFRACTIONr_sphericity_free70.0555501
X-RAY DIFFRACTIONr_sphericity_bonded31.192577947
LS refinement shellResolution: 2.401→2.464 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 995 -
Rwork0.293 19824 -
all-20819 -
obs--99.18 %
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)
10.0297-0.0123-0.02020.01310.00250.0249-0.00120.00260.00220.00150.0020.00220.00230.0022-0.00080.0902-0.0009-0.00380.09030.00270.00286.989493.231517.0504
20.03070.0051-0.00120.0058-0.00780.0157-0.0035-0.0001-0.0075-0.00320.0016-0.0004-0.00210.00190.00190.09170.0001-0.00290.089-0.00230.004-76.914853.1188-41.3621
30.06210.02130.00780.00980.00870.0156-0.00540.00130.0207-0.00090.00180.00720.0063-0.00220.00370.0928-0.0010.00140.08940.00110.007-38.3559145.6313-17.2205
40.05230.00560.00230.006-0.00830.0148-0.0016-0.0035-0.013900.0021-0.0012-0.00510.0009-0.00050.09260.0001-0.00070.09040.00310.0039-76.701553.68186.7267
50.05320.01880.00970.01710.0070.0163-0.00110.00020.0083-0.0008-0.0016-0.00130.0029-0.00070.00280.09080.00090.00090.0893-0.00180.0036-38.1718143.752530.5609
60.05310.0436-0.01170.050.00210.0138-0.00060.00430.0002-0.00490.0074-0.0080.0009-0.0057-0.00680.0899-0.00040.00140.09120.00080.0049-36.380386.4858-46.9079
70.03070.02280.02070.02540.0140.01870.0002-0.00160.0034-0.0006-0.0010.0098-0.00360.00420.00080.0898-0.00130.00150.0920.00070.0068-79.1427112.2782-23.1238
80.03530.0307-0.01440.0392-0.00530.0230.0010.0019-0.00390.00050.0012-0.0102-0.0006-0.0037-0.00220.08940.0006-0.00080.0921-0.00010.0042-36.766886.159952.2281
90.02030.0199-0.01520.0234-0.00690.0320.0009-0.00580.0022-0.00130.00240.00110.00380.0037-0.00330.08920.0012-0.00030.0935-0.00240.0008-36.299187.40780.8809
100.03290.01440.0210.02970.00860.0291-0.0006-0.00540.0003-0.00050.00050.0045-0.0008-0.000500.08910.00090.00180.09110.00160.0009-78.8279110.475924.4877
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 603
2X-RAY DIFFRACTION2B40 - 604
3X-RAY DIFFRACTION3C39 - 604
4X-RAY DIFFRACTION4D40 - 604
5X-RAY DIFFRACTION5E39 - 604
6X-RAY DIFFRACTION6F40 - 604
7X-RAY DIFFRACTION7G40 - 604
8X-RAY DIFFRACTION8H39 - 604
9X-RAY DIFFRACTION9I40 - 604
10X-RAY DIFFRACTION10J40 - 604

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