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- PDB-7kv6: Surface glycan-binding protein B from Bacteroides fluxus in compl... -

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Basic information

Entry
Database: PDB / ID: 7kv6
TitleSurface glycan-binding protein B from Bacteroides fluxus in complex with mixed-linkage glucotriose
ComponentsPKD domain protein
KeywordsSUGAR BINDING PROTEIN / CBM / lectin
Function / homologyPKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold / GUANIDINE / PKD domain protein
Function and homology information
Biological speciesBacteroides fluxus YIT 12057 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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: PKD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8084
Polymers31,1861
Non-polymers6233
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.980, 77.222, 148.379
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11AAA-1360-

HOH

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Components

#1: Protein PKD domain protein


Mass: 31185.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fluxus YIT 12057 (bacteria)
Gene: HMPREF9446_00613 / Production host: Escherichia coli (E. coli) / References: UniProt: F3PPH3
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH5N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1 M MES pH6.6, 0.2 M ammonium sulfate, 20 % (w/v) PEG5000MME, 0.1M guanidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→74.19 Å / Num. obs: 43047 / % possible obs: 95.5 % / Redundancy: 11.8 % / CC1/2: 0.999 / Net I/σ(I): 34.4
Reflection shellResolution: 1.61→1.64 Å / Num. unique obs: 2197 / CC1/2: 0.907

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→74.189 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / Cross valid method: FREE R-VALUE / ESU R: 0.08 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2043 2197 5.104 %
Rwork0.1782 40850 -
all0.18 --
obs-43047 95.437 %
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: 31.631 Å2
Baniso -1Baniso -2Baniso -3
1--0.937 Å20 Å20 Å2
2--3.521 Å20 Å2
3----2.584 Å2
Refinement stepCycle: LAST / Resolution: 1.6→74.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 42 331 2280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132020
X-RAY DIFFRACTIONr_bond_other_d0.0370.0171703
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.6692759
X-RAY DIFFRACTIONr_angle_other_deg2.4641.5953968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3335257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72725.05787
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.028102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21815272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.674152
X-RAY DIFFRACTIONr_chiral_restr0.0850.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022298
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02412
X-RAY DIFFRACTIONr_nbd_refined0.2030.2321
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.21533
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2975
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2823
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1550.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1640.24
X-RAY DIFFRACTIONr_nbd_other0.1920.219
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.120.220
X-RAY DIFFRACTIONr_mcbond_it2.5883.2281027
X-RAY DIFFRACTIONr_mcbond_other2.5593.2251026
X-RAY DIFFRACTIONr_mcangle_it3.2544.8311284
X-RAY DIFFRACTIONr_mcangle_other3.2644.8331285
X-RAY DIFFRACTIONr_scbond_it3.7763.405993
X-RAY DIFFRACTIONr_scbond_other3.7753.405993
X-RAY DIFFRACTIONr_scangle_it5.2355.0111475
X-RAY DIFFRACTIONr_scangle_other5.2335.0111476
X-RAY DIFFRACTIONr_lrange_it6.52139.4392282
X-RAY DIFFRACTIONr_lrange_other6.29438.1582191
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
1.609-1.6510.3051070.30921940.30932820.7110.68470.10970.28
1.651-1.6960.3321150.31625170.31732060.5960.6482.09610.28
1.696-1.7450.3311630.2727170.27331370.7410.79191.80750.23
1.745-1.7990.2821560.24227910.24430180.8490.86197.64740.205
1.799-1.8580.2371530.20927960.21129570.8990.91499.72950.18
1.858-1.9230.2241270.19427210.19528610.9220.93699.54560.163
1.923-1.9960.2211500.19425910.19627510.9230.93199.63650.166
1.996-2.0770.2331210.19225210.19426590.920.93799.36070.166
2.077-2.1690.2411310.18424070.18725500.9240.94199.52940.166
2.169-2.2750.2141260.17523190.17724520.9440.95299.71450.158
2.275-2.3980.191300.16321870.16523240.9520.95899.69880.151
2.398-2.5430.2481270.17520310.1821940.9340.9598.35920.164
2.543-2.7190.191030.17219790.17320880.9520.95599.71260.168
2.719-2.9360.197820.16718440.16819280.9530.9699.89630.171
2.936-3.2160.196860.16517020.16717950.9560.9699.610.176
3.216-3.5950.179870.16615280.16716270.9660.96799.26240.182
3.595-4.1490.174820.1613610.16114490.9690.96899.58590.187
4.149-5.0780.162730.14211630.14312430.9730.97699.43680.177
5.078-7.1640.244460.1919370.1949860.9470.96299.69570.239
7.164-74.1890.197320.2115430.215900.9610.94797.45760.313

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