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- PDB-6fx2: crystal structure of Pholiota squarrosa lectin in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 6fx2
Titlecrystal structure of Pholiota squarrosa lectin in complex with a decasaccharide
Componentslectin
KeywordsSUGAR BINDING PROTEIN / lectin / decasaccharide
Function / homologyLectin
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_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

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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)12,3584
Polymers9,4232
Non-polymers2,9362
Water2,432135
1
A: lectin
hetero molecules

A: lectin
hetero molecules

A: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0856
Polymers14,1343
Non-polymers4,9523
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11270 Å2
ΔGint53 kcal/mol
Surface area8030 Å2
MethodPISA
2
B: lectin
hetero molecules

B: lectin
hetero molecules

B: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9896
Polymers14,1343
Non-polymers3,8563
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11100 Å2
ΔGint36 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.862, 101.862, 101.862
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-265-

HOH

21B-269-

HOH

31B-270-

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 beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...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: 1650.503 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/6,9,8/[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][a1221m-1a_1-5]/1-2-3-4-2-4-2-5-6/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 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+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...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: 1285.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/6,7,6/[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][a1221m-1a_1-5]/1-2-3-4-2-5-6/a4-b1_a6-g1_b4-c1_c6-d1_d2-e1_e4-f1WURCSPDB2Glycan 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+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.77 % / Description: little diamond
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 3.2M Na malonate pH 5.0

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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→36.01 Å / Num. obs: 19497 / % possible obs: 100 % / Redundancy: 32.2 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.012 / Net I/σ(I): 45.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 29.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 1048 / CC1/2: 0.968 / Rpim(I) all: 0.144 / % 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: PhosLDodeca

Resolution: 1.7→36.01 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.454 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.075 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18773 976 5 %RANDOM
Rwork0.16374 ---
obs0.16498 18521 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.558 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms646 0 201 135 982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02883
X-RAY DIFFRACTIONr_bond_other_d0.0020.02715
X-RAY DIFFRACTIONr_angle_refined_deg1.892.1871233
X-RAY DIFFRACTIONr_angle_other_deg0.94931701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.405581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.9292430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.4771588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.275152
X-RAY DIFFRACTIONr_chiral_restr0.1060.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021796
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02156
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_it2.0012.431330
X-RAY DIFFRACTIONr_mcbond_other1.9462.421329
X-RAY DIFFRACTIONr_mcangle_it2.8163.614409
X-RAY DIFFRACTIONr_mcangle_other2.8163.62410
X-RAY DIFFRACTIONr_scbond_it2.9013.084553
X-RAY DIFFRACTIONr_scbond_other2.8993.083553
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.344.529824
X-RAY DIFFRACTIONr_long_range_B_refined5.91434.523932
X-RAY DIFFRACTIONr_long_range_B_other5.77133.704904
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 66 -
Rwork0.257 1353 -
obs--100 %

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