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- PDB-2cgy: STRUCTURE OF HELIX POMATIA AGGLUTININ WITH FORSMANN ANTIGEN -

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Basic information

Entry
Database: PDB / ID: 2cgy
TitleSTRUCTURE OF HELIX POMATIA AGGLUTININ WITH FORSMANN ANTIGEN
ComponentsAGGLUTININ
KeywordsSUGAR BINDING PROTEIN / LECTIN / SNAIL
Function / homology
Function and homology information


carbohydrate binding / cell adhesion / metal ion binding
Similarity search - Function
Immunoglobulin-like - #2080 / H-type lectin domain / H-type lectin domain superfamily / H-type lectin domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Forssman antigen fragment / Agglutinin
Similarity search - Component
Biological speciesHELIX POMATIA (Roman snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSanchez, J.-F. / Lescar, J. / Audfray, A. / Gautier, C. / Chazalet, V. / Gagnon, J. / Breton, C. / Imberty, A. / Mitchell, E.P.
CitationJournal: Glycobiology / Year: 2007
Title: Structural Basis for Recognition of Breast and Colon Cancer Epitopes Tn Antigen and Forssman Disaccharide by Helix Pomatia Lectin.
Authors: Lescar, J. / Sanchez, J.-F. / Audfray, A. / Coll, J. / Breton, C. / Mitchell, E.P. / Imberty, A.
History
DepositionMar 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9853
Polymers11,3401
Non-polymers6462
Water181
1
A: AGGLUTININ
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)71,91218
Polymers68,0396
Non-polymers3,87412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area13680 Å2
ΔGint-58.5 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.019, 62.019, 106.642
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein AGGLUTININ /


Mass: 11339.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SIGMA-ALDRICH / Source: (natural) HELIX POMATIA (Roman snail) / Organ: ALBUMIN GLAND / References: UniProt: Q2F1K8
#2: Polysaccharide 2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose / Forssman antigen fragment


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Forssman antigen fragment
DescriptorTypeProgram
DGalpNAca1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc]{[(3+1)][a-D-GalpNAc]{}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.3 Å3/Da / Density % sol: 47.2 %
Crystal growMethod: vapor diffusion, hanging drop
Details: HANGING DROP METHOD WITH PRECIPITATION SOLUTION CONTAINING LITHIUM SULPHATE (2 M) AND AMMONIUM SULPHATE (3.5 M) IN SODIUM CITRATE BUFFER (1.5M, PH 6.5) AND 10MM OF FORSMANN LIGAND.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 8, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 2945 / % possible obs: 87.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.1
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CE6

2ce6


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.857 / SU B: 16.219 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R Free: 0.512 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.32 132 4.5 %RANDOM
Rwork0.262 ---
obs0.265 2792 88.1 %-
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: 54.29 Å2
Baniso -1Baniso -2Baniso -3
1--3.92 Å2-1.96 Å20 Å2
2---3.92 Å20 Å2
3---5.88 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms767 0 43 1 811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022831
X-RAY DIFFRACTIONr_bond_other_d0.0020.02710
X-RAY DIFFRACTIONr_angle_refined_deg1.2422.0091137
X-RAY DIFFRACTIONr_angle_other_deg0.733.0031646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.086599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02154
X-RAY DIFFRACTIONr_nbd_refined0.190.2153
X-RAY DIFFRACTIONr_nbd_other0.2090.2858
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.2527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.221
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0130.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3221.5499
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.5972810
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.753332
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3484.5327
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: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.656 9
Rwork0.325 199

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