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- PDB-7kv3: Surface glycan-binding protein A from Bacteroides thetaiotaomicro... -

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Basic information

Entry
Database: PDB / ID: 7kv3
TitleSurface glycan-binding protein A from Bacteroides thetaiotaomicron in complex with laminarihexaose
ComponentsRagB/SusD family nutrient uptake outer membrane protein
KeywordsSUGAR BINDING PROTEIN / SusD / Tetratricopeptide repeat / CBM
Function / homologySusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / beta-cellohexaose / RagB/SusD domain protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsTamura, K. / Brumer, H. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota.
Authors: Tamura, K. / Dejean, G. / Van Petegem, F. / Brumer, H.
History
DepositionNov 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: RagB/SusD family nutrient uptake outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4393
Polymers59,3521
Non-polymers1,0872
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.024, 72.937, 101.484
Angle α, β, γ (deg.)90.000, 105.644, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11AAA-981-

HOH

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Components

#1: Protein RagB/SusD family nutrient uptake outer membrane protein


Mass: 59352.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: DW011_12550, DW780_14665, DWY18_18425, GAN67_20195, GAN98_19115
Production host: Escherichia coli (E. coli) / References: UniProt: A0A173VPY3
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellohexaose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a3-b1_b3-c1_c3-d1_d3-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 46.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1 M bis-tris pH 6.5, 0.2 M lithium sulfate, 25 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.05→39.45 Å / Num. obs: 33221 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 0.992 / Net I/σ(I): 8
Reflection shellResolution: 2.05→2.11 Å / Num. unique obs: 1639 / CC1/2: 0.668

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→39.447 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: FREE R-VALUE / ESU R: 0.173 / ESU R Free: 0.155
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2041 1639 4.934 %
Rwork0.1569 31582 -
all0.159 --
obs-33221 98.778 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.868 Å2
Baniso -1Baniso -2Baniso -3
1-0.815 Å20 Å2-0.473 Å2
2---0.018 Å20 Å2
3----0.461 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 72 295 4160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133970
X-RAY DIFFRACTIONr_bond_other_d0.0360.0173440
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.6685405
X-RAY DIFFRACTIONr_angle_other_deg2.6821.5987989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04323.17224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59315619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2661521
X-RAY DIFFRACTIONr_chiral_restr0.0770.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024410
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02853
X-RAY DIFFRACTIONr_nbd_refined0.1970.2804
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.23210
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21967
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2268
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.240.28
X-RAY DIFFRACTIONr_nbd_other0.2480.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1240.29
X-RAY DIFFRACTIONr_mcbond_it1.7442.1191865
X-RAY DIFFRACTIONr_mcbond_other1.7412.1181864
X-RAY DIFFRACTIONr_mcangle_it2.6093.1652326
X-RAY DIFFRACTIONr_mcangle_other2.613.1662327
X-RAY DIFFRACTIONr_scbond_it2.3042.3262105
X-RAY DIFFRACTIONr_scbond_other2.3022.3222101
X-RAY DIFFRACTIONr_scangle_it3.6283.4043079
X-RAY DIFFRACTIONr_scangle_other3.6243.3993074
X-RAY DIFFRACTIONr_lrange_it4.61724.5214706
X-RAY DIFFRACTIONr_lrange_other4.58324.3484661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.05-2.1030.2481240.23223190.23324610.8820.87799.26860.228
2.103-2.1610.2771210.2122500.21423890.8780.89599.24660.201
2.161-2.2230.2471180.20122060.20423470.8990.90699.020.19
2.223-2.2910.2211120.18421040.18622670.9090.92797.75030.172
2.291-2.3660.1931270.16720410.16922040.9350.93998.36660.153
2.366-2.4490.23950.16120330.16421390.9250.94799.48570.147
2.449-2.5410.2111080.15719450.1620650.9420.94999.41890.141
2.541-2.6440.1991090.15918590.16119800.9440.94699.39390.143
2.644-2.7610.232840.15517900.15819010.9380.95198.57970.138
2.761-2.8950.219900.15316850.15618180.9360.95197.63480.137
2.895-3.0510.175710.14116600.14217400.9580.96699.48280.128
3.051-3.2350.201710.14615490.14916310.9460.96199.32560.135
3.235-3.4560.226730.15514840.15815680.9320.95399.29850.145
3.456-3.7310.177670.13913200.14114270.9620.96297.19690.136
3.731-4.0830.154610.12612760.12713440.9680.97499.47920.124
4.083-4.5590.176530.12311340.12512050.9620.97598.50620.122
4.559-5.2530.173500.1349950.13610650.9620.96998.12210.135
5.253-6.4050.248360.1668550.1699070.9360.95998.23590.163
6.405-8.9410.176420.1496810.157290.9570.96899.1770.15
8.941-39.4470.18270.1813950.1814270.9650.96698.8290.198

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