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- PDB-6jk2: Crystal structure of a mini fungal lectin, PhoSL -

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Basic information

Entry
Database: PDB / ID: 6jk2
TitleCrystal structure of a mini fungal lectin, PhoSL
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / PhoSL / core-fucosylated chitobiose
Function / homologymetal ion binding / Lectin
Function and homology information
Biological speciesPholiota squarrosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.06 Å
AuthorsLou, Y.C. / Chou, C.C. / Yeh, H.H. / Chien, C.Y. / Sushant, S. / Chen, C. / Hsu, C.H.
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structural insights into the role of N-terminal integrity in PhoSL for core-fucosylated N-glycan recognition.
Authors: Lou, Y.C. / Tu, C.F. / Chou, C.C. / Yeh, H.H. / Chien, C.Y. / Sadotra, S. / Chen, C. / Yang, R.B. / Hsu, C.H.
History
DepositionFeb 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 24, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.3Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6443
Polymers4,4521
Non-polymers1922
Water77543
1
A: Lectin
hetero molecules

A: Lectin
hetero molecules

A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9329
Polymers13,3563
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area4990 Å2
ΔGint-84 kcal/mol
Surface area6770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.475, 42.475, 37.704
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein/peptide Lectin


Mass: 4451.946 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pholiota squarrosa (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3B6UEU4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulfate, 30% w/v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1.7 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 1.06→30 Å / Num. obs: 17498 / % possible obs: 99.3 % / Redundancy: 21.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.036 / Net I/σ(I): 77.87
Reflection shellResolution: 1.06→1.1 Å / Redundancy: 19.1 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 14.41 / Num. unique obs: 1685 / CC1/2: 0.993 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.06→21.25 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.504 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15798 895 5.1 %RANDOM
Rwork0.13577 ---
obs0.13695 16487 98.96 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.7 Å
Displacement parametersBiso mean: 17.174 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.09 Å2-0 Å2
2---0.19 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.06→21.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms314 0 10 43 367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.013333
X-RAY DIFFRACTIONr_bond_other_d0.0010.017277
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.653459
X-RAY DIFFRACTIONr_angle_other_deg1.5611.598640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.555539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.64223.12516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.251542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.267151
X-RAY DIFFRACTIONr_chiral_restr0.0810.241
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02373
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0274
X-RAY DIFFRACTIONr_mcbond_it1.0321.572159
X-RAY DIFFRACTIONr_mcbond_other0.9981.558157
X-RAY DIFFRACTIONr_mcangle_it1.4622.362197
X-RAY DIFFRACTIONr_mcangle_other1.4492.36197
X-RAY DIFFRACTIONr_scbond_it1.9411.837174
X-RAY DIFFRACTIONr_scbond_other1.8891.804166
X-RAY DIFFRACTIONr_scangle_other2.452.642250
X-RAY DIFFRACTIONr_long_range_B_refined2.81119.645364
X-RAY DIFFRACTIONr_long_range_B_other2.47818.629351
X-RAY DIFFRACTIONr_rigid_bond_restr1.7223610
LS refinement shellResolution: 1.062→1.089 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.145 47 -
Rwork0.163 1156 -
obs--91.76 %

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