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- PDB-6t0q: Pleurotus Ostreatus Lectin (POL), apo form -

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Basic information

Entry
Database: PDB / ID: 6t0q
TitlePleurotus Ostreatus Lectin (POL), apo form
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Lectin / POL / galactose / Carbohydrate-Binding Module (CBM)
Function / homologymetal ion binding / Lectin
Function and homology information
Biological speciesPleurotus ostreatus (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.05 Å
AuthorsDestefanis, L. / Perduca, M. / Bovi, M. / Monaco, H.L. / Capaldi, S.
CitationJournal: Glycobiology / Year: 2020
Title: Structure and properties of the oyster mushroom (Pleurotus ostreatus) lectin.
Authors: Perduca, M. / Destefanis, L. / Bovi, M. / Galliano, M. / Munari, F. / Assfalg, M. / Ferrari, F. / Monaco, H.L. / Capaldi, S.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / 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_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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.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 / _chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / pdbx_branch_scheme / 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 / pdbx_validate_close_contact / struct_asym / struct_conn
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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _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_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _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_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,78711
Polymers37,0471
Non-polymers1,74010
Water5,008278
1
A: Lectin
hetero molecules

A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,57422
Polymers74,0952
Non-polymers3,47920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area6880 Å2
ΔGint-7 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.070, 153.070, 145.811
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lectin / Lectin 1


Mass: 37047.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pleurotus ostreatus (oyster mushroom) / References: UniProt: E7E2M2

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 284 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes 0.1 M pH 7.5, 0.8 M K/Na tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.05→132.562 Å / Num. all: 63266 / Num. obs: 63266 / % possible obs: 99.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 27.56 Å2 / Rpim(I) all: 0.02 / Rrim(I) all: 0.071 / Rsym value: 0.068 / Net I/av σ(I): 9.4 / Net I/σ(I): 25.9 / Num. measured all: 790176
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.05-2.1613.20.38211941790740.1070.3950.387.499.7
2.16-2.2912.60.3012.410829286160.0880.3140.3019.699.8
2.29-2.4511.60.19249360380640.0580.20.19212.199.7
2.45-2.6513.10.1425.49939376110.040.1470.14216.899.9
2.65-2.912.90.098.29001570000.0260.0940.0924.199.9
2.9-3.2411.80.0611.87468863510.0180.0630.0633.299.8
3.24-3.7413.20.044157475256670.0120.0460.04449.1100
3.74-4.5811.90.03716.85739748360.0110.0390.0375599.8
4.58-6.4812.50.03318.54765138040.010.0350.03357.4100
6.48-63.88211.10.0317.32496822430.010.0320.0354.199.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
SCALA3.3.21data scaling
PDB_EXTRACT3.25data extraction
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.05→29.771 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 16.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1866 3208 5.08 %
Rwork0.1718 59991 -
obs0.1726 63199 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.97 Å2 / Biso mean: 29.8576 Å2 / Biso min: 14.78 Å2
Refinement stepCycle: final / Resolution: 2.05→29.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 110 278 2917
Biso mean--57.58 36.5 -
Num. residues----340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.05-2.08060.22381460.1838254499
2.0806-2.11310.17451290.1703257499
2.1131-2.14780.22911530.16362538100
2.1478-2.18480.19291470.16342552100
2.1848-2.22450.17851430.16572586100
2.2245-2.26730.19151430.16432539100
2.2673-2.31360.17071470.16582564100
2.3136-2.36380.20021210.15932597100
2.3638-2.41880.20271260.169257399
2.4188-2.47930.18561120.172612100
2.4793-2.54630.22891360.17632598100
2.5463-2.62110.20251320.17552567100
2.6211-2.70570.19981420.18472605100
2.7057-2.80230.22121300.18112601100
2.8023-2.91440.18941430.19992602100
2.9144-3.0470.21791290.1972624100
3.047-3.20740.21631410.1906259899
3.2074-3.40810.18241560.19212614100
3.4081-3.67080.20161530.18022608100
3.6708-4.03940.16821340.16752669100
4.0394-4.62210.15911300.13782678100
4.6221-5.81620.13421600.14042698100
5.8162-29.7710.18941550.18312850100
Refinement TLS params.Method: refined / Origin x: 20.3492 Å / Origin y: 82.3767 Å / Origin z: 23.2827 Å
111213212223313233
T0.1215 Å20.0336 Å2-0.0171 Å2-0.1813 Å20.0157 Å2--0.1504 Å2
L0.405 °2-0.247 °2-0.0994 °2-0.5545 °20.0415 °2--0.4593 °2
S-0.0069 Å °-0.0785 Å °-0.0299 Å °0.0281 Å °0.0439 Å °0.0371 Å °0.0437 Å °0.1276 Å °0.0093 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA34 - 373
2X-RAY DIFFRACTION1allA400 - 603
3X-RAY DIFFRACTION1allS1 - 278

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