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- PDB-1g9f: CRYSTAL STRUCTURE OF THE SOYBEAN AGGLUTININ IN A COMPLEX WITH A B... -

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Basic information

Entry
Database: PDB / ID: 1g9f
TitleCRYSTAL STRUCTURE OF THE SOYBEAN AGGLUTININ IN A COMPLEX WITH A BIANTENNARY BLOOD GROUP ANTIGEN ANALOG
ComponentsLECTIN
KeywordsSUGAR BINDING PROTEIN / JELLY-ROLL FOLD / LEGUME LECTIN
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsButs, L. / Hamelryck, T.W. / Dao-Thi, M.-H. / Loris, R. / Wyns, L. / Etzler, M.E.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Weak protein-protein interactions in lectins: the crystal structure of a vegetative lectin from the legume Dolichos biflorus.
Authors: Buts, L. / Dao-Thi, M.H. / Loris, R. / Wyns, L. / Etzler, M. / Hamelryck, T.
#1: Journal: Biochemistry / Year: 1997
Title: X-ray crystallographic studies of unique cross-linked lattices between four isomeric biantennary oligosaccharides and soybean agglutinin
Authors: Olsen, L.R. / Dessen, A. / Gupta, D. / Sabesan, S. / Sacchettini, J.C. / Brewer, C.F.
#2: Journal: Biochemistry / Year: 1995
Title: X-ray crystal structure of the soybean agglutinin cross-linked with a biantennary analog of the blood group I carbohydrate antigen
Authors: Dessen, A. / Gupta, D. / Sabesan, S. / Brewer, C.F. / Sacchettini, J.C.
History
DepositionNov 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: 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

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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)29,0265
Polymers27,5961
Non-polymers1,4304
Water1629
1
A: LECTIN
hetero molecules

A: LECTIN
hetero molecules

A: LECTIN
hetero molecules

A: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,10420
Polymers110,3834
Non-polymers5,72116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-y+1,x-1/2,z+1/41
crystal symmetry operation6_556x,-y+1/2,-z+5/41
crystal symmetry operation8_666-y+1,-x+1,-z+11
Unit cell
Length a, b, c (Å)122.640, 122.640, 90.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: - monomer B: symmetry -X,-Y,Z translation (245.28,0,0) - monomer C: symmetry -Y,-X,-Z translation (122.64,122.64,90,56) - monomer D: symmetry Y,X,-Z translation (122.64,122.64,90.56)

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LECTIN / / AGGLUTININ / SBA


Mass: 27595.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / Organ: SEED / References: UniProt: P05046

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Sugars , 2 types, 2 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]beta-D-galactopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2[DGalpb1-4DGlcpNAcb1-3]DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-1-2-1/a2-b1_a3-d1_b4-c1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 11 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.08 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: protein,carbohydrate,HEPES,CaCl(2),MnCl(2),NaCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-7 mg/mlprotein1reservoir
2100 mMsodium citrate1reservoir
38-12 %(w/v)PEG60001reservoir
40.2-0.4 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 72368 / Num. obs: 57894 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 2.9 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.25 Å / Mean I/σ(I) obs: 3.7
Reflection
*PLUS
Num. all: 57894 / Num. obs: 19716 / % possible obs: 80 % / Num. measured all: 72368
Reflection shell
*PLUS
% possible obs: 72.7 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: soybean agglutinin

Resolution: 2.5→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1969940.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1125 10.3 %RANDOM
Rwork0.19 ---
all0.19 10942 --
obs0.19 10942 89.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.72 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---0.86 Å20 Å2
3---1.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 92 9 1894
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it2.261.5
X-RAY DIFFRACTIONc_mcangle_it3.352
X-RAY DIFFRACTIONc_scbond_it3.822
X-RAY DIFFRACTIONc_scangle_it5.072.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 143 -
Rwork0.247 0 -
obs-1457 80.2 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.19 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.306 / Rfactor Rwork: 0.247

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