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- PDB-7bfy: Structure of the apo form of the N terminal domain of Bc2L-C lect... -

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Basic information

Entry
Database: PDB / ID: 7bfy
TitleStructure of the apo form of the N terminal domain of Bc2L-C lectin (1-131)
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / lectins / drug resistance / glycomimetics / anti-adhesive therapy / drug design / fragment-based screening
Function / homologyLectin Bc2l-C, N-terminal / : / Bc2l-C, N-terminal domain / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / identical protein binding / Lectin
Function and homology information
Biological speciesBurkholderia cenocepacia J2315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLal, K. / Bermeo, R. / Imberty, A. / Varrot, A.
Funding support France, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765581 France
CitationJournal: Chemistry / Year: 2021
Title: Prediction and Validation of a Druggable Site on Virulence Factor of Drug Resistant Burkholderia cenocepacia*.
Authors: Lal, K. / Bermeo, R. / Cramer, J. / Vasile, F. / Ernst, B. / Imberty, A. / Bernardi, A. / Varrot, A. / Belvisi, L.
History
DepositionJan 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 31, 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

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Assembly

Deposited unit
A: Lectin


Theoretical massNumber of molelcules
Total (without water)13,7451
Polymers13,7451
Non-polymers00
Water2,468137
1
A: Lectin

A: Lectin

A: Lectin


Theoretical massNumber of molelcules
Total (without water)41,2343
Polymers41,2343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area5570 Å2
ΔGint-44 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.987, 42.987, 94.678
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

21A-239-

HOH

31A-302-

HOH

41A-335-

HOH

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Components

#1: Protein Lectin


Mass: 13744.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia J2315 (bacteria)
Gene: BCAM0185 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EH86
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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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: 1.81 Å3/Da / Density meas: 32.01 Mg/m3 / Density % sol: 33.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5.5 mg/ml of protein, 1.2 M sodium citrate, at 292 K temperature and cryoprotected with 2.5 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.754
11-K, -H, -L20.246
ReflectionResolution: 1.5→19.97 Å / Num. obs: 15915 / % possible obs: 99.9 % / Redundancy: 16.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.021 / Rrim(I) all: 0.085 / Net I/σ(I): 21.7 / Num. measured all: 261006 / Scaling rejects: 4
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
1.5-1.5315.50.454126938200.9350.1230.4715.9100
8.22-19.9713.70.0621325970.9880.020.06536.291.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6tig

6tig


Resolution: 1.5→19.97 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.437 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.015 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1778 762 4.8 %RANDOM
Rwork0.1488 ---
obs0.1502 15120 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.28 Å2 / Biso mean: 15.084 Å2 / Biso min: 8.54 Å2
Baniso -1Baniso -2Baniso -3
1--2.99 Å2-0 Å2-0 Å2
2---2.99 Å2-0 Å2
3---5.98 Å2
Refinement stepCycle: final / Resolution: 1.5→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 0 142 1091
Biso mean---27.43 -
Num. residues----131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.013976
X-RAY DIFFRACTIONr_bond_other_d0.0010.017915
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.6321340
X-RAY DIFFRACTIONr_angle_other_deg1.5051.5632104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8715132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64222.90331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.04315136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.952152
X-RAY DIFFRACTIONr_chiral_restr0.0860.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021110
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02210
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 54 -
Rwork0.191 1155 -
all-1209 -
obs--100 %

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