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- PDB-6a86: Pholiota squarrosa lectin -

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Basic information

Entry
Database: PDB / ID: 6a86
TitlePholiota squarrosa lectin
Componentslectin
KeywordsSUGAR BINDING PROTEIN / Lectin / Trimer / Fucose
Function / homology(3R)-butane-1,3-diol / Lectin (PhoSL)
Function and homology information
Biological speciesPholiota squarrosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYamasaki, K. / Yamasaki, T. / Kubota, T.
CitationJournal: Glycobiology / Year: 2019
Title: Structural basis for specific recognition of core fucosylation in N-glycans by Pholiota squarrosa lectin (PhoSL).
Authors: Yamasaki, K. / Kubota, T. / Yamasaki, T. / Nagashima, I. / Shimizu, H. / Terada, R.I. / Nishigami, H. / Kang, J. / Tateno, M. / Tateno, H.
History
DepositionJul 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Nov 22, 2023Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lectin
B: lectin
C: lectin
D: lectin
E: lectin
F: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,00610
Polymers26,6466
Non-polymers3604
Water3,333185
1
A: lectin
B: lectin
C: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5936
Polymers13,3233
Non-polymers2703
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-28 kcal/mol
Surface area6570 Å2
MethodPISA
2
D: lectin
E: lectin
F: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4134
Polymers13,3233
Non-polymers901
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-28 kcal/mol
Surface area6430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.280, 145.280, 39.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein/peptide
lectin / PhoSL


Mass: 4440.958 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Pholiota squarrosa (fungus) / References: UniProt: A0A384E107*PLUS
#2: Chemical
ChemComp-BU4 / (3R)-butane-1,3-diol


Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.8 M potassium-sodium phosphate (pH 7.0), 5% 1,3-butanediol

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 28520 / % possible obs: 98.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 42.2
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.391

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XZK

5xzk


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.012 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24852 1356 4.8 %RANDOM
Rwork0.19575 ---
obs0.19826 26967 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.655 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 24 185 2064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.021956
X-RAY DIFFRACTIONr_bond_other_d0.0030.021712
X-RAY DIFFRACTIONr_angle_refined_deg2.2551.9282694
X-RAY DIFFRACTIONr_angle_other_deg1.0993.0013970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3615.042240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.59724.61578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6115258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1250.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212159
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02409
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.393.153950
X-RAY DIFFRACTIONr_mcbond_other3.3723.149949
X-RAY DIFFRACTIONr_mcangle_it4.7854.6821179
X-RAY DIFFRACTIONr_mcangle_other4.7864.6891180
X-RAY DIFFRACTIONr_scbond_it4.053.5261006
X-RAY DIFFRACTIONr_scbond_other3.9873.5261006
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5095.1421512
X-RAY DIFFRACTIONr_long_range_B_refined7.82337.9082258
X-RAY DIFFRACTIONr_long_range_B_other7.80637.6972225
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 91 -
Rwork0.232 1983 -
obs--98.48 %

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