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- PDB-6zfc: Fucose-binding lectin from Burkholderia ambifaria (BamBL) in comp... -

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Basic information

Entry
Database: PDB / ID: 6zfc
TitleFucose-binding lectin from Burkholderia ambifaria (BamBL) in complex with a fucosyl derivative
Componentsbacterial lectin from Burkholderia ambifaria
KeywordsSUGAR BINDING PROTEIN / fucose-binding lectin / glycomimetics
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / Chem-QJB / Fucose-binding lectin protein
Function and homology information
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKuhaudomlarp, S. / Gillon, E. / Fragai, M. / Cerofolini, L. / Giuntini, S. / Denis, M. / Santarsia, S. / Valori, C. / Dondoni, A. / Fallarini, S. ...Kuhaudomlarp, S. / Gillon, E. / Fragai, M. / Cerofolini, L. / Giuntini, S. / Denis, M. / Santarsia, S. / Valori, C. / Dondoni, A. / Fallarini, S. / Lombardi, G. / Nativi, C. / Imberty, A.
Funding support France, Italy, 5items
OrganizationGrant numberCountry
French National Research AgencyANR-AAPG-2017 France
French National Research AgencyANR-15-IDEX02 France
French National Research AgencyANR-17-EURE-0003 France
Italian Ministry of EducationPRIN 2015 Italy
Italian Ministry of EducationProgetto Dipartimenti di Eccellenza 2018-2022 Italy
CitationJournal: Chem Sci / Year: 2020
Title: Fucosylated ubiquitin and orthogonally glycosylated mutant A28C: conceptually new ligands for Burkholderia ambifaria lectin (BambL).
Authors: Kuhaudomlarp, S. / Cerofolini, L. / Santarsia, S. / Gillon, E. / Fallarini, S. / Lombardi, G. / Denis, M. / Giuntini, S. / Valori, C. / Fragai, M. / Imberty, A. / Dondoni, A. / Nativi, C.
History
DepositionJun 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: bacterial lectin from Burkholderia ambifaria
B: bacterial lectin from Burkholderia ambifaria
C: bacterial lectin from Burkholderia ambifaria
D: bacterial lectin from Burkholderia ambifaria
E: bacterial lectin from Burkholderia ambifaria
F: bacterial lectin from Burkholderia ambifaria
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,75618
Polymers56,3236
Non-polymers4,43312
Water7,728429
1
A: bacterial lectin from Burkholderia ambifaria
B: bacterial lectin from Burkholderia ambifaria
C: bacterial lectin from Burkholderia ambifaria
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3789
Polymers28,1613
Non-polymers2,2176
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-24 kcal/mol
Surface area11480 Å2
MethodPISA
2
D: bacterial lectin from Burkholderia ambifaria
E: bacterial lectin from Burkholderia ambifaria
F: bacterial lectin from Burkholderia ambifaria
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3789
Polymers28,1613
Non-polymers2,2176
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-24 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.092, 49.163, 115.098
Angle α, β, γ (deg.)90.000, 91.360, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
bacterial lectin from Burkholderia ambifaria


Mass: 9387.166 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (strain ATCC BAA-244 / AMMD) (bacteria)
Gene: Bamb_5415 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0B4G1
#2: Chemical
ChemComp-QJB / 2-[(2~{S},3~{S},4~{R},4~{a}~{S},10~{a}~{S})-2-methyl-3,4-bis(oxidanyl)-3,4,4~{a},10~{a}-tetrahydro-2~{H}-pyrano[2,3-b][1,4]benzoxathiin-7-yl]-~{N}-(3-oxidanylpropyl)ethanamide


Mass: 369.433 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C17H23NO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: 200 mM trisodium citrate, 100 mM sodium acetate pH 5.0 and 24% PEG 8000, 1% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.65→45.25 Å / Num. obs: 72307 / % possible obs: 98.1 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.036 / Rrim(I) all: 0.095 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.687.11.262470734940.6270.5091.361.596.5
9.04-45.216.50.03431534880.9990.0140.03733.899.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZW0

3zw0


Resolution: 1.65→45.21 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.113 / SU ML: 0.068 / SU R Cruickshank DPI: 0.0917 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 3534 4.9 %RANDOM
Rwork0.1767 ---
obs0.1782 68772 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.13 Å2 / Biso mean: 22.618 Å2 / Biso min: 13.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.49 Å2
2---1.27 Å2-0 Å2
3---1.49 Å2
Refinement stepCycle: final / Resolution: 1.65→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3962 0 262 435 4659
Biso mean--26.44 31.28 -
Num. residues----522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124429
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183559
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.6586100
X-RAY DIFFRACTIONr_angle_other_deg1.4951.5758229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1525532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7721.349215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95915533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9861524
X-RAY DIFFRACTIONr_chiral_restr0.0810.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021066
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 295 -
Rwork0.316 4890 -
all-5185 -
obs--96.2 %

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