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- PDB-2x2s: Crystal structure of Sclerotinia sclerotiorum agglutinin SSA -

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Basic information

Entry
Database: PDB / ID: 2x2s
TitleCrystal structure of Sclerotinia sclerotiorum agglutinin SSA
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: 1.6 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 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

Downloads & links

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Assembly

Deposited unit
A: AGGLUTININ
B: AGGLUTININ
C: AGGLUTININ
D: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2156
Polymers67,0304
Non-polymers1842
Water12,791710
1
C: AGGLUTININ
D: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6073
Polymers33,5152
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-9.4 kcal/mol
Surface area12880 Å2
MethodPISA
2
A: AGGLUTININ
B: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6073
Polymers33,5152
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-9.9 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.318, 127.318, 86.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.55313, 0.57456, -0.60327), (0.595, -0.77929, -0.19666), (-0.58312, -0.25017, -0.77291)17.69346, 14.12032, 60.88956
2given(0.84757, 0.53066, 0.00392), (0.5306, -0.84755, 0.01067), (0.00899, -0.00697, -0.99994)0.30995, 0.31765, -17.53764
3given(-0.77096, 0.18907, 0.60817), (-0.08182, -0.97641, 0.19983), (0.6316, 0.1043, 0.76824)100.13724, 19.96608, -39.42391

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Components

#1: Protein
AGGLUTININ / AGGLUTININ SSA


Mass: 16757.600 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) SCLEROTINIA SCLEROTIORUM (fungus) / References: UniProt: A7XUK7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 3.03 Å3/Da / Density % sol: 59.4 % / Description: NONE
Crystal growDetails: 2.1 M SODIUM CHLORIDE, 0.1 M SODIUM ACETATE, PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9686
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.6→68 Å / Num. obs: 100976 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 16.68 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.6 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL GENERATED BY PHYRE SERVER

Resolution: 1.6→110.43 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.535 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.065 / 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
Rfree0.16197 4061 4 %RANDOM
Rwork0.14001 ---
obs0.1409 96905 96.08 %-
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: 22.309 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å2-0 Å2
2--0.42 Å2-0 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.6→110.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4651 0 12 710 5373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225191
X-RAY DIFFRACTIONr_bond_other_d0.0010.023427
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9457144
X-RAY DIFFRACTIONr_angle_other_deg0.89738494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5345708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18525.43221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61215846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8731512
X-RAY DIFFRACTIONr_chiral_restr0.0990.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02996
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_it1.61133254
X-RAY DIFFRACTIONr_mcbond_other0.54231309
X-RAY DIFFRACTIONr_mcangle_it2.53545305
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.01331937
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.14741796
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: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 237 -
Rwork0.212 5289 -
obs--71.61 %
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)
10.271-0.1794-0.03571.40690.50370.61820.0455-0.0002-0.02470.0214-0.01230.0230.0191-0.0471-0.03320.04950.0085-0.00220.0116-0.00480.022443.8269.4398.468
20.4387-0.2830.00171.18870.43350.7725-0.051-0.025-0.00050.06560.0496-0.01260.0645-0.04170.00140.03140.01410.00910.0244-0.00340.019441.7613225.793
30.5035-0.3829-0.1721.11190.17940.7606-0.02860.02710.01990.00660.03030.0199-0.0067-0.1573-0.00180.01490.00580.00040.04030.00020.012642.11815.327-25.718
40.4351-0.1223-0.01831.0712-0.22280.90450.0383-0.0065-0.0152-0.115-0.0280.0369-0.11290.0824-0.01030.0947-0.0183-0.01120.00900.002474.9314.9470.427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 153
2X-RAY DIFFRACTION2B2 - 153
3X-RAY DIFFRACTION3C2 - 153
4X-RAY DIFFRACTION4D2 - 153

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