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- PDB-6fx3: crystal structure of Pholiota squarrosa lectin in complex with a ... -

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Entry
Database: PDB / ID: 6fx3
Titlecrystal structure of Pholiota squarrosa lectin in complex with a dodecasaccharide
Componentslectin
KeywordsSUGAR BINDING PROTEIN / lectin / dodecasaccharide
Function / homologymetal ion binding / Lectin
Function and homology information
Biological speciesPholiota squarrosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCabanettes, A. / Varrot, A.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Recognition of Complex Core-Fucosylated N-Glycans by a Mini Lectin.
Authors: Cabanettes, A. / Perkams, L. / Spies, C. / Unverzagt, C. / Varrot, A.
History
DepositionMar 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: 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.title / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_struct_special_symmetry / 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_alt_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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _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 2.1May 1, 2024Group: 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 2.2Nov 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
B: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9414
Polymers9,4232
Non-polymers3,5182
Water2,468137
1
A: lectin
hetero molecules

A: lectin
hetero molecules

A: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9596
Polymers14,1343
Non-polymers5,8253
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12400 Å2
ΔGint70 kcal/mol
Surface area8380 Å2
MethodPISA
2
B: lectin
hetero molecules

B: lectin
hetero molecules

B: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8636
Polymers14,1343
Non-polymers4,7293
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12190 Å2
ΔGint55 kcal/mol
Surface area7320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.744, 101.744, 101.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-262-

HOH

21B-273-

HOH

31B-274-

HOH

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Components

#1: Protein/peptide lectin


Mass: 4711.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pholiota squarrosa (fungus) / Plasmid: pet39a-TEV / Details (production host): pet39a-TEV-PhosL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): star / References: UniProt: A0A3B6UEU4*PLUS
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamine


Type: oligosaccharide / Mass: 1941.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/7,10,9/[a2122h-1b_1-5_1*N=^ZN=N_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1a_1-5]/1-2-3-4-2-4-2-5-6-7/a4-b1_a6-j1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1_h6-i2WURCSPDB2Glycan 1.1.0
[][<N2>]{[(1+1)][b-D-Glcp1N2NAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamine


Type: oligosaccharide / Mass: 1576.425 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/7,8,7/[a2122h-1b_1-5_1*N=^ZN=N_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1a_1-5]/1-2-3-4-2-5-6-7/a4-b1_a6-h1_b4-c1_c6-d1_d2-e1_e4-f1_f6-g2WURCSPDB2Glycan 1.1.0
[][<N2>]{[(1+1)][b-D-Glcp1N2NAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 48.59 % / Description: little diamond
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 3.4 M Na malonate pH5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→41.54 Å / Num. obs: 19409 / % possible obs: 100 % / Redundancy: 17.3 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.018 / Net I/σ(I): 32.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 16.9 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1020 / CC1/2: 0.917 / Rpim(I) all: 0.239 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDS20171111data reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PhoslOcta

Resolution: 1.7→41 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.5 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18661 973 5 %RANDOM
Rwork0.15733 ---
obs0.15883 18434 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.598 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms648 0 241 137 1026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02931
X-RAY DIFFRACTIONr_bond_other_d0.0020.02748
X-RAY DIFFRACTIONr_angle_refined_deg2.0642.2311305
X-RAY DIFFRACTIONr_angle_other_deg0.96431786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.214581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.7922430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.1931590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2152
X-RAY DIFFRACTIONr_chiral_restr0.1110.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021814
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02158
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_it1.7052.163330
X-RAY DIFFRACTIONr_mcbond_other1.6882.156329
X-RAY DIFFRACTIONr_mcangle_it2.5123.219409
X-RAY DIFFRACTIONr_mcangle_other2.5133.224410
X-RAY DIFFRACTIONr_scbond_it2.9682.859600
X-RAY DIFFRACTIONr_scbond_other2.9632.859600
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5084.181897
X-RAY DIFFRACTIONr_long_range_B_refined6.51931.631940
X-RAY DIFFRACTIONr_long_range_B_other6.10330.661909
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 68 -
Rwork0.246 1334 -
obs--100 %

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