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- PDB-7umj: Crystal structure of recombinant Solieria filiformis lectin (rSfL) -

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Basic information

Entry
Database: PDB / ID: 7umj
TitleCrystal structure of recombinant Solieria filiformis lectin (rSfL)
ComponentsLectin SfL-1
KeywordsSUGAR BINDING PROTEIN / lectin / red algae / Solieria filiformis
Function / homologyOAA-family lectin sugar binding domain / OAA-family lectin sugar binding domain / mannose binding / Lectin SfL-1
Function and homology information
Biological speciesSolieria filiformis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsChaves, R.P. / Bezerra, E.H.S. / da Silva, F.M.S. / Carneiro, R.F. / Sampaio, A.H. / Rocha, B.A.M. / Nagano, C.S.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)429166/2018-4 Brazil
CitationJournal: Biochimie / Year: 2023
Title: Structural study and antimicrobial and wound healing effects of lectin from Solieria filiformis (Kutzing) P.W.Gabrielson.
Authors: Chaves, R.P. / Dos Santos, A.K.B. / Andrade, A.L. / Pinheiro, A.A. / Silva, J.M.S. / da Silva, F.M.S. / de Sousa, J.P. / Barroso Neto, I.L. / Bezerra, E.H.S. / Abreu, J.O. / de Carvalho, F.C. ...Authors: Chaves, R.P. / Dos Santos, A.K.B. / Andrade, A.L. / Pinheiro, A.A. / Silva, J.M.S. / da Silva, F.M.S. / de Sousa, J.P. / Barroso Neto, I.L. / Bezerra, E.H.S. / Abreu, J.O. / de Carvalho, F.C.T. / de Sousa, O.V. / de Sousa, B.L. / da Rocha, B.A.M. / Silva, A.L.C. / do Nascimento Neto, L.G. / de Vasconcelos, M.A. / Teixeira, E.H. / Carneiro, R.F. / Sampaio, A.H. / Nagano, C.S.
History
DepositionApr 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Lectin SfL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7652
Polymers30,6691
Non-polymers961
Water5,657314
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)48.054, 62.430, 90.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Lectin SfL-1


Mass: 30669.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solieria filiformis (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: C0HL89
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 100 mM sodium chloride, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.46→45.35 Å / Num. obs: 80687 / % possible obs: 87.93 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.77 Å2 / CC1/2: 0.997 / Net I/σ(I): 5.3
Reflection shellResolution: 1.88→1.94 Å / Redundancy: 2 % / Num. unique obs: 22337 / CC1/2: 0.941 / % possible all: 95.77

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoPROCdata reduction
autoPROCdata processing
SCALAdata scaling
MOLREPphasing
PHENIX1.13refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GU8

4gu8


Resolution: 1.88→45.35 Å / SU ML: 0.208 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6089
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2309 2016 4.81 %
Rwork0.1825 39881 -
obs0.1848 41897 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.89 Å2
Refinement stepCycle: LAST / Resolution: 1.88→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 5 314 2270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532000
X-RAY DIFFRACTIONf_angle_d0.80492717
X-RAY DIFFRACTIONf_chiral_restr0.051275
X-RAY DIFFRACTIONf_plane_restr0.0052365
X-RAY DIFFRACTIONf_dihedral_angle_d16.4821283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.28551570.24672760X-RAY DIFFRACTION95.11
1.93-1.980.31061330.23062805X-RAY DIFFRACTION95.98
1.98-2.040.29651350.22562810X-RAY DIFFRACTION96.18
2.04-2.10.31021370.20392821X-RAY DIFFRACTION96.41
2.1-2.180.2641460.19662803X-RAY DIFFRACTION96.69
2.18-2.270.20241470.20232852X-RAY DIFFRACTION97.78
2.27-2.370.24831490.19972834X-RAY DIFFRACTION98.12
2.37-2.490.28341370.1922902X-RAY DIFFRACTION98.25
2.49-2.650.2581440.19292840X-RAY DIFFRACTION98.13
2.65-2.850.24531400.18992882X-RAY DIFFRACTION98.31
2.85-3.140.21731490.17952896X-RAY DIFFRACTION99.38
3.14-3.60.20971460.15742867X-RAY DIFFRACTION98.82
3.6-4.530.18361410.1462900X-RAY DIFFRACTION99.41
4.53-45.350.19451550.17432909X-RAY DIFFRACTION99.35

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