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- PDB-7kv2: Surface glycan-binding protein A from Bacteroides thetaiotaomicron -

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Basic information

Entry
Database: PDB / ID: 7kv2
TitleSurface glycan-binding protein A from Bacteroides thetaiotaomicron
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 / RagB/SusD domain protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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)59,8337
Polymers59,3521
Non-polymers4816
Water6,197344
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)54.830, 71.685, 75.068
Angle α, β, γ (deg.)90.000, 105.099, 90.000
Int Tables number4
Space group name H-MP1211

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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: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1 M bis-tris pH6.5, 0.2M lithium sulfate, 25 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→38.26 Å / Num. obs: 51588 / % possible obs: 99.1 % / Redundancy: 6.3 % / CC1/2: 0.993 / Net I/σ(I): 10
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 2482 / CC1/2: 0.462

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→38.26 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.105
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.194 2482 4.811 %
Rwork0.1638 49106 -
all0.165 --
obs-51588 98.89 %
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: 25.718 Å2
Baniso -1Baniso -2Baniso -3
1-0.403 Å20 Å2-0.434 Å2
2---0.073 Å20 Å2
3----0.084 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3831 0 31 344 4206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133981
X-RAY DIFFRACTIONr_bond_other_d0.0360.0173466
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.6495419
X-RAY DIFFRACTIONr_angle_other_deg2.3641.5768042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6045473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44223.117231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49715627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1511522
X-RAY DIFFRACTIONr_chiral_restr0.0860.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024506
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02876
X-RAY DIFFRACTIONr_nbd_refined0.2070.2863
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.23294
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21973
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.21516
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2265
X-RAY DIFFRACTIONr_metal_ion_refined0.120.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.210
X-RAY DIFFRACTIONr_nbd_other0.2050.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.214
X-RAY DIFFRACTIONr_mcbond_it2.312.6591892
X-RAY DIFFRACTIONr_mcbond_other2.312.6591891
X-RAY DIFFRACTIONr_mcangle_it3.1073.9712365
X-RAY DIFFRACTIONr_mcangle_other3.1073.9722366
X-RAY DIFFRACTIONr_scbond_it2.6912.7982089
X-RAY DIFFRACTIONr_scbond_other2.6912.7992090
X-RAY DIFFRACTIONr_scangle_it3.9664.1113054
X-RAY DIFFRACTIONr_scangle_other3.9664.1123055
X-RAY DIFFRACTIONr_lrange_it5.16230.7734803
X-RAY DIFFRACTIONr_lrange_other5.00230.5084736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8460.3910.2643381X-RAY DIFFRACTION89.7854
1.846-1.8970.2771890.2443491X-RAY DIFFRACTION98.8185
1.897-1.9520.2541920.2113436X-RAY DIFFRACTION99.78
1.952-2.0120.2561820.1913324X-RAY DIFFRACTION99.8007
2.012-2.0780.2381870.1823259X-RAY DIFFRACTION99.8551
2.078-2.1510.2061650.173139X-RAY DIFFRACTION99.7585
2.151-2.2320.2211440.1633030X-RAY DIFFRACTION99.7799
2.232-2.3230.191600.1582929X-RAY DIFFRACTION99.7739
2.323-2.4260.1961420.1552825X-RAY DIFFRACTION99.899
2.426-2.5440.1861440.1512643X-RAY DIFFRACTION99.8209
2.544-2.6820.1651280.1492590X-RAY DIFFRACTION99.67
2.682-2.8440.2081080.1522420X-RAY DIFFRACTION99.5276
2.844-3.040.1841220.1612275X-RAY DIFFRACTION99.7918
3.04-3.2830.2141170.1692102X-RAY DIFFRACTION99.373
3.283-3.5960.18960.1621978X-RAY DIFFRACTION99.4247
3.596-4.0190.187800.1461769X-RAY DIFFRACTION99.892
4.019-4.6380.148770.1351564X-RAY DIFFRACTION99.214
4.638-5.6750.168700.1551325X-RAY DIFFRACTION99.359
5.675-8.0010.207540.1771042X-RAY DIFFRACTION99.8178
8.001-38.260.133340.133584X-RAY DIFFRACTION98.0952

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