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- PDB-6jk3: Crystal structure of a mini fungal lectin, PhoSL in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6jk3
TitleCrystal structure of a mini fungal lectin, PhoSL in complex with core-fucosylated chitobiose
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 / MOLECULAR REPLACEMENT / Resolution: 1.12 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Dec 6, 2023Group: Database references / Category: citation / citation_author
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
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin
B: Lectin
C: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,43610
Polymers13,3563
Non-polymers2,0807
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-24 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.295, 61.295, 67.916
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein/peptide Lectin


Mass: 4451.946 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pholiota squarrosa (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: A0A3B6UEU4
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 1.6 M Sodium citrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.12→30 Å / Num. obs: 50196 / % possible obs: 99.6 % / Redundancy: 12.4 % / CC1/2: 0.943 / Rmerge(I) obs: 0.062 / Net I/σ(I): 42.85
Reflection shellResolution: 1.12→1.16 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 4797 / CC1/2: 0.738 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JK2

6jk2


Resolution: 1.12→27.43 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.87 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14506 2324 5 %RANDOM
Rwork0.12093 ---
obs0.12211 44030 92.14 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.238 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0 Å2-0 Å2
2--0.35 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.12→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 141 162 1245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131118
X-RAY DIFFRACTIONr_bond_other_d0.0010.018945
X-RAY DIFFRACTIONr_angle_refined_deg1.621.8131541
X-RAY DIFFRACTIONr_angle_other_deg1.4531.7452207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4555117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.08223.12548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.58315126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.665153
X-RAY DIFFRACTIONr_chiral_restr0.0830.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02234
X-RAY DIFFRACTIONr_mcbond_it0.9331.493477
X-RAY DIFFRACTIONr_mcbond_other0.9171.488475
X-RAY DIFFRACTIONr_mcangle_it1.1612.243591
X-RAY DIFFRACTIONr_mcangle_other1.1462.242591
X-RAY DIFFRACTIONr_scbond_it1.6291.873640
X-RAY DIFFRACTIONr_scbond_other1.6281.874641
X-RAY DIFFRACTIONr_scangle_other2.1342.719950
X-RAY DIFFRACTIONr_long_range_B_refined3.06620.5751185
X-RAY DIFFRACTIONr_long_range_B_other2.58219.6031145
X-RAY DIFFRACTIONr_rigid_bond_restr2.09432057
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 29 -
Rwork0.264 636 -
obs--18.21 %

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