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- PDB-6t1d: Pleurotus Ostreatus Lectin (POL), compelx with melibiose -

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Basic information

Entry
Database: PDB / ID: 6t1d
TitlePleurotus Ostreatus Lectin (POL), compelx with melibiose
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Lectin / POL / galactose / Carbohydrate-Binding Module (CBM)
Function / homologymetal ion binding / alpha-melibiose / Lectin
Function and homology information
Biological speciesPleurotus ostreatus (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 4, 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 / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 23, 2024Group: Structure summary / Category: 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
B: Lectin
C: Lectin
D: Lectin
E: Lectin
F: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,92830
Polymers224,3396
Non-polymers4,58924
Water5,008278
1
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,30910
Polymers74,7802
Non-polymers1,5308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lectin
D: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,30910
Polymers74,7802
Non-polymers1,5308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Lectin
F: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,30910
Polymers74,7802
Non-polymers1,5308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.605, 136.421, 110.022
Angle α, β, γ (deg.)90.000, 112.370, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 36 through 78 or resid 80 through 373))
21(chain B and (resid 36 through 78 or resid 80 through 373))
31(chain C and (resid 36 through 78 or resid 80 through 373))
41(chain D and (resid 36 through 78 or resid 80 through 373))
51(chain E and (resid 36 through 78 or resid 80 through 373))
61(chain F and (resid 36 through 78 or resid 80 through 373))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSASNASN(chain A and (resid 36 through 78 or resid 80 through 373))AA36 - 7819 - 61
12THRTHRALAALA(chain A and (resid 36 through 78 or resid 80 through 373))AA80 - 37363 - 356
21CYSCYSASNASN(chain B and (resid 36 through 78 or resid 80 through 373))BB36 - 7819 - 61
22THRTHRALAALA(chain B and (resid 36 through 78 or resid 80 through 373))BB80 - 37363 - 356
31CYSCYSASNASN(chain C and (resid 36 through 78 or resid 80 through 373))CC36 - 7819 - 61
32THRTHRALAALA(chain C and (resid 36 through 78 or resid 80 through 373))CC80 - 37363 - 356
41CYSCYSASNASN(chain D and (resid 36 through 78 or resid 80 through 373))DD36 - 7819 - 61
42THRTHRALAALA(chain D and (resid 36 through 78 or resid 80 through 373))DD80 - 37363 - 356
51CYSCYSASNASN(chain E and (resid 36 through 78 or resid 80 through 373))EE36 - 7819 - 61
52THRTHRALAALA(chain E and (resid 36 through 78 or resid 80 through 373))EE80 - 37363 - 356
61CYSCYSASNASN(chain F and (resid 36 through 78 or resid 80 through 373))FF36 - 7819 - 61
62THRTHRALAALA(chain F and (resid 36 through 78 or resid 80 through 373))FF80 - 37363 - 356

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Components

#1: Protein
Lectin / Lectin 1


Mass: 37389.875 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurotus ostreatus (oyster mushroom) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: E7E2M2
#2: Polysaccharide
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose / alpha-melibiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-melibiose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


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

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 K thiocyanate, 30% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.09→47.67 Å / Num. obs: 88942 / % possible obs: 92.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.34 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.096 / Rrim(I) all: 0.179 / Net I/σ(I): 6.6
Reflection shell

Num. unique obs: 4447 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.093-2.4073.60.821158800.4670.510.9681.765.5
7.172-101.7443.30.055144950.9960.0350.06515.899

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T0Q

6t0q


Resolution: 2.2→29.948 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2651 4407 5.01 %
Rwork0.2118 83567 -
obs0.2145 87974 58.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.19 Å2 / Biso mean: 41.3375 Å2 / Biso min: 5.84 Å2
Refinement stepCycle: final / Resolution: 2.2→29.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15102 0 222 278 15602
Biso mean--59.73 32.48 -
Num. residues----2028
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9280X-RAY DIFFRACTION6.42TORSIONAL
12B9280X-RAY DIFFRACTION6.42TORSIONAL
13C9280X-RAY DIFFRACTION6.42TORSIONAL
14D9280X-RAY DIFFRACTION6.42TORSIONAL
15E9280X-RAY DIFFRACTION6.42TORSIONAL
16F9280X-RAY DIFFRACTION6.42TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2003-2.22530.3397140.27422656
2.2253-2.25140.3137210.30823067
2.2514-2.27890.4848190.30814058
2.2789-2.30770.3128310.313647510
2.3077-2.33810.4678380.311354312
2.3381-2.37010.4052200.287863613
2.3701-2.40390.3741340.314766214
2.4039-2.43980.367530.306974716
2.4398-2.47790.2955660.323492020
2.4779-2.51850.3863550.3291123726
2.5185-2.56190.3719900.3009153332
2.5619-2.60850.3357810.3194190839
2.6085-2.65860.3511110.3208230048
2.6586-2.71290.30131530.3069262555
2.7129-2.77180.32561490.3023291460
2.7718-2.83620.30411630.2971313866
2.8362-2.90710.32041890.2835331770
2.9071-2.98560.32821760.2703358075
2.9856-3.07340.32471860.2441392581
3.0734-3.17250.30892360.252424990
3.1725-3.28580.31552600.2396472699
3.2858-3.41710.3222400.2341480999
3.4171-3.57240.24912760.20274739100
3.5724-3.76040.25572650.19284743100
3.7604-3.99550.26492470.17784817100
3.9955-4.30320.21782470.16454768100
4.3032-4.73470.1922780.1569478399
4.7347-5.41630.20912920.1575473999
5.4163-6.81080.24542280.1834484099
6.8108-29.9480.21811890.1886491899
Refinement TLS params.Method: refined / Origin x: 16.9598 Å / Origin y: 0.0959 Å / Origin z: 30.212 Å
111213212223313233
T0.2424 Å2-0.0026 Å2-0.0953 Å2-0.1373 Å2-0.0223 Å2--0.1906 Å2
L0.2715 °20.0819 °2-0.094 °2-0.4832 °2-0.0335 °2--0.1985 °2
S0.0028 Å °0.0765 Å °-0.1056 Å °-0.5025 Å °0.0457 Å °0.274 Å °-0.0509 Å °-0.0764 Å °-0.0057 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA36 - 373
2X-RAY DIFFRACTION1allA401 - 502
3X-RAY DIFFRACTION1allB36 - 373
4X-RAY DIFFRACTION1allB401 - 502
5X-RAY DIFFRACTION1allC36 - 373
6X-RAY DIFFRACTION1allC401 - 502
7X-RAY DIFFRACTION1allD36 - 373
8X-RAY DIFFRACTION1allD401 - 502
9X-RAY DIFFRACTION1allE36 - 373
10X-RAY DIFFRACTION1allE401 - 502
11X-RAY DIFFRACTION1allF36 - 373
12X-RAY DIFFRACTION1allF401 - 502
13X-RAY DIFFRACTION1allS1 - 278

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