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- PDB-6fx1: Crystal structure of Pholiota squarrosa lectin in complex with an... -

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Basic information

Entry
Database: PDB / ID: 6fx1
TitleCrystal structure of Pholiota squarrosa lectin in complex with an octasaccharide
Componentslectin
KeywordsSUGAR BINDING PROTEIN / lectin / octasaccharide
Function / homologymetal ion binding / MALONATE ION / 3-OXOOCTANOIC ACID / Lectin
Function and homology information
Biological speciesPholiota squarrosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.1Jul 18, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Aug 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: Advisory / Atomic model ...Advisory / 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_unobs_or_zero_occ_atoms / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.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 2.2Oct 16, 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
D: lectin
E: lectin
F: lectin
G: lectin
H: lectin
I: lectin
J: lectin
K: lectin
L: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,15037
Polymers56,53512
Non-polymers14,61525
Water5,693316
1
A: lectin
B: lectin
C: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,33310
Polymers14,1343
Non-polymers4,1997
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: lectin
E: lectin
F: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,97211
Polymers14,1343
Non-polymers3,8388
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: lectin
H: lectin
I: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9719
Polymers14,1343
Non-polymers3,8376
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: lectin
K: lectin
L: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8747
Polymers14,1343
Non-polymers2,7404
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.000, 95.593, 110.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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Protein/peptide , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein/peptide
lectin


Mass: 4711.271 Da / Num. of mol.: 12
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) / Variant (production host): star / References: UniProt: A0A3B6UEU4*PLUS

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Sugars , 5 types, 12 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1- ...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: 1123.029 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/5,6,5/[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][a1221m-1a_1-5]/1-2-3-4-2-5/a4-b1_a6-f1_b4-c1_c6-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp1N2NAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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: 1488.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/5,8,7/[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][a1221m-1a_1-5]/1-2-3-4-2-4-2-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][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]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 919.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/5,5,4/[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][a1221m-1a_1-5]/1-2-3-4-5/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp1N2NAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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: 1285.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/5,7,6/[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][a1221m-1a_1-5]/1-2-3-4-4-2-5/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp1N2NAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 757.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/4,4,3/[a2122h-1b_1-5_1*N=^ZN=N_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-2-3-4/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp1N2NAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 329 molecules

#7: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H2O4
#8: Chemical ChemComp-OOA / 3-OXOOCTANOIC ACID


Mass: 158.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.78 % / Description: diamant
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 3.2 M Na malonate pH5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.1→47.88 Å / Num. obs: 56993 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 18.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDS20160617data reduction
Aimless0.5.27data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PhosL

Resolution: 2.1→47.88 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.229 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21925 2785 4.9 %RANDOM
Rwork0.18391 ---
obs0.18567 54161 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.71 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----2.18 Å2
Refinement stepCycle: 1 / Resolution: 2.1→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3787 0 984 316 5087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024967
X-RAY DIFFRACTIONr_bond_other_d0.0020.024021
X-RAY DIFFRACTIONr_angle_refined_deg1.8512.1436909
X-RAY DIFFRACTIONr_angle_other_deg0.95639520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7845479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.11524.545176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08615509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.863156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214745
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02897
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_it1.6222.7461946
X-RAY DIFFRACTIONr_mcbond_other1.6232.7461945
X-RAY DIFFRACTIONr_mcangle_it2.6394.0842415
X-RAY DIFFRACTIONr_mcangle_other2.6394.0852416
X-RAY DIFFRACTIONr_scbond_it1.9833.5793021
X-RAY DIFFRACTIONr_scbond_other1.9833.583022
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8845.2894495
X-RAY DIFFRACTIONr_long_range_B_refined5.10238.1045008
X-RAY DIFFRACTIONr_long_range_B_other5.10238.1045009
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 221 -
Rwork0.236 3929 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.90283.0606-1.33465.6912-2.04541.52920.0920.039-0.0420.2345-0.02250.05790.1433-0.1822-0.06950.1278-0.0658-0.03090.0808-0.00770.02922.4591-28.4389-11.1998
21.2543-0.2062-0.88081.54540.89014.35050.0338-0.0056-0.11930.11710.00860.05610.4246-0.1321-0.04240.2209-0.1057-0.04420.0661-0.00090.067922.0477-40.4598-11.7389
31.4698-1.67730.15766.26340.93291.51610.11850.2333-0.0133-0.1489-0.0398-0.16180.2691-0.0344-0.07870.1638-0.075-0.02830.1152-0.00740.035228.2299-34.7595-20.1606
42.8562-2.14211.46634.9941-2.30963.32580.15090.1096-0.0744-0.1411-0.09130.13910.2497-0.1946-0.05960.0729-0.0710.00190.0976-0.01050.004721.1052-19.45427.4492
50.8649-0.31840.44811.09171.24496.5310.0457-0.01660.0576-0.05580.02650.1976-0.0555-0.303-0.07220.018-0.02670.00420.08770.02090.098120.6281-7.39337.9479
61.22351.1402-0.00726.42391.14090.96710.1107-0.18620.00330.2071-0.0121-0.0290.1558-0.1251-0.09860.0485-0.0303-0.00840.12210.03120.018925.5862-13.14117.1014
76.39590.71390.19441.3030.23282.59030.04490.12730.1085-0.16550.0893-0.0385-0.0905-0.0154-0.13430.0563-0.02420.00270.04380.02390.025433.5842-4.9541-18.0763
84.4213-3.6591-3.02365.18913.4675.2142-0.1419-0.16990.07060.10570.2655-0.1248-0.09910.4682-0.12370.0328-0.0449-0.00770.10860.01240.016141.1313-2.3331-8.4535
90.9947-0.46250.950.80640.06966.40750.0423-0.01630.1734-0.00240.10750.0546-0.3048-0.1917-0.14980.04190.00610.04080.04550.04330.098329.27570.4691-8.3702
106.5881-2.11181.41851.8914-0.05113.18740.1154-0.3892-0.2530.27350.05560.10370.3703-0.211-0.1710.3041-0.0922-0.02380.07440.06610.088630.9575-42.935615.9154
114.39281.54011.9462.40921.96723.4126-0.03590.1592-0.30180.01930.2148-0.09940.52890.3761-0.17890.38380.0247-0.08820.08970.05170.122139.3495-46.02117.5713
121.85830.2488-0.85080.6727-1.20476.9320.0875-0.0754-0.32560.02040.07270.09740.4206-0.3127-0.16030.3686-0.0853-0.05630.03530.04410.175327.8103-48.23326.1135
1300000000000000-00.1816000.181600.1816000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 39
2X-RAY DIFFRACTION2B1 - 39
3X-RAY DIFFRACTION3C-1 - 39
4X-RAY DIFFRACTION4D1 - 39
5X-RAY DIFFRACTION5E1 - 39
6X-RAY DIFFRACTION6F1 - 39
7X-RAY DIFFRACTION7G-1 - 39
8X-RAY DIFFRACTION8H1 - 39
9X-RAY DIFFRACTION9I1 - 39
10X-RAY DIFFRACTION10J-1 - 39
11X-RAY DIFFRACTION11K2 - 39
12X-RAY DIFFRACTION12L2 - 39
13X-RAY DIFFRACTION13N1 - 39

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