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- PDB-2x2t: CRYSTAL STRUCTURE OF SCLEROTINIA SCLEROTIORUM AGGLUTININ SSA in c... -

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Basic information

Entry
Database: PDB / ID: 2x2t
TitleCRYSTAL STRUCTURE OF SCLEROTINIA SCLEROTIORUM AGGLUTININ SSA in complex with Gal-beta1,3-Galnac
ComponentsAGGLUTININ
KeywordsCELL ADHESION / FUNGAL LECTIN / BETA-TREFOIL DOMAIN
Function / homologyRicin-type beta-trefoil lectin domain-like / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / carbohydrate binding / Mainly Beta / Agglutinin
Function and homology information
Biological speciesSCLEROTINIA SCLEROTIORUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSulzenbacher, G. / Roig-Zamboni, V. / Peumans, W.J. / Rouge, P. / Van Damme, E.J.M. / Bourne, Y.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure of the Galnac/Gal-Specific Agglutinin from the Phytopathogenic Ascomycete Sclerotinia Sclerotiorum Reveals Novel Adaptation of a Beta-Trefoil Domain
Authors: Sulzenbacher, G. / Roig-Zamboni, V. / Peumans, W.J. / Rouge, P. / Van Damme, E.J.M. / Bourne, Y.
History
DepositionJan 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: PROVIDED BY DEPOSITOR
Remark 700 SHEET DETERMINATION METHOD: PROVIDED BY DEPOSITOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9148
Polymers16,7581
Non-polymers1,1567
Water3,045169
1
A: AGGLUTININ
hetero molecules

A: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,82716
Polymers33,5152
Non-polymers2,31214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area4850 Å2
ΔGint-65 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.458, 51.458, 295.987
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1159-

PG4

21A-2079-

HOH

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Components

#1: Protein AGGLUTININ / / AGGLUTININ SSA


Mass: 16757.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SCLEROTINIA SCLEROTIORUM (fungus) / References: UniProt: A7XUK7
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.38 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growDetails: 1.26 M AMMONIUM SULFATE, 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.97→59 Å / Num. obs: 17040 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.3 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X2S

2x2s


Resolution: 1.97→49.33 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.166 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B-FACTORS, CONTAINING RESIDUAL AND TLS COMPONENT HAVE BEEN DEPOSITED
RfactorNum. reflection% reflectionSelection details
Rfree0.19514 1228 7.2 %RANDOM
Rwork0.16304 ---
obs0.16526 15811 96.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.768 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.42 Å2-0 Å2
2--0.83 Å2-0 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.97→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 0 63 169 1409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221332
X-RAY DIFFRACTIONr_bond_other_d0.0010.02867
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.981825
X-RAY DIFFRACTIONr_angle_other_deg0.89932148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7815169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.48925.35756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85515203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.387153
X-RAY DIFFRACTIONr_chiral_restr0.0920.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211457
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
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_it0.7151.5800
X-RAY DIFFRACTIONr_mcbond_other0.1941.5322
X-RAY DIFFRACTIONr_mcangle_it1.26421300
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8663532
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8414.5518
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 98 -
Rwork0.214 1127 -
obs--98.39 %
Refinement TLS params.Method: refined / Origin x: 21.6716 Å / Origin y: -19.8032 Å / Origin z: 10.1223 Å
111213212223313233
T0.0013 Å2-0.0094 Å20.0021 Å2-0.0499 Å2-0.0127 Å2--0.0534 Å2
L1.5494 °2-0.0221 °2-0.409 °2-0.8226 °2-0.0261 °2--2.8772 °2
S0.0508 Å °0.049 Å °0.0256 Å °-0.0051 Å °-0.0498 Å °-0.0435 Å °-0.0458 Å °0.0536 Å °-0.001 Å °

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