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- PDB-7kv1: Surface glycan-binding protein A from Bacteroides uniformis -

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Basic information

Entry
Database: PDB / ID: 7kv1
TitleSurface glycan-binding protein A from Bacteroides uniformis
ComponentsSusD family protein
KeywordsSUGAR BINDING PROTEIN / SusD / Tetratricopeptide repeat / CBM
Function / homologySusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / membrane / COBALT HEXAMMINE(III) / SusD family protein
Function and homology information
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 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
A: SusD family protein
B: SusD family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,7888
Polymers121,0702
Non-polymers7186
Water9,908550
1
A: SusD family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7583
Polymers60,5351
Non-polymers2232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SusD family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0305
Polymers60,5351
Non-polymers4944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.270, 53.583, 126.850
Angle α, β, γ (deg.)90.000, 93.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SusD family protein


Mass: 60535.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (strain ATCC 8492 / DSM 6597 / CIP 103695 / JCM 5828 / NCTC 13054 / VPI 0061) (bacteria)
Strain: ATCC 8492 / DSM 6597 / CIP 103695 / JCM 5828 / NCTC 13054 / VPI 0061
Gene: BACUNI_01488 / Production host: Escherichia coli (E. coli) / References: UniProt: A7V1Q0
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1 M bis-tris pH 5.3, 0.2 M ammonium acetate, 22 % (w/v) PEG3350, 0.01 M hexamine cobalt (III) chloride

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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: 1.86→41.81 Å / Num. obs: 77609 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.996 / Net I/σ(I): 10.3
Reflection shellResolution: 1.86→1.89 Å / Num. unique obs: 3967 / CC1/2: 0.578

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→41.81 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.263 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 3967 5.1 %RANDOM
Rwork0.1668 ---
obs0.1689 73642 89.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.57 Å2 / Biso mean: 26.494 Å2 / Biso min: 13.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20.53 Å2
2---1.26 Å20 Å2
3---0.94 Å2
Refinement stepCycle: final / Resolution: 1.86→41.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7323 0 40 550 7913
Biso mean--29.07 33.64 -
Num. residues----913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137540
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176604
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.65110252
X-RAY DIFFRACTIONr_angle_other_deg1.4221.58415257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945903
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26322.847432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.719151180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9731544
X-RAY DIFFRACTIONr_chiral_restr0.0740.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028548
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021696
LS refinement shellResolution: 1.86→1.903 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.317 335 -
Rwork0.274 5692 -
obs--94.26 %

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