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- PDB-1fay: WINGED BEAN ACIDIC LECTIN COMPLEXED WITH METHYL-ALPHA-D-GALACTOSE... -

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Basic information

Entry
Database: PDB / ID: 1fay
TitleWINGED BEAN ACIDIC LECTIN COMPLEXED WITH METHYL-ALPHA-D-GALACTOSE (MONOCLINIC FORM)
ComponentsACIDIC LECTIN
KeywordsSUGAR BINDING PROTEIN / LEGUME LECTIN / GLYCOSYLATED PROTEIN / H-ANTIGENIC SPECIFICITY / AGGLUTININ
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Legume lectin / : / 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
methyl alpha-D-galactopyranoside / : / : / Winged bean acidic lectin
Similarity search - Component
Biological speciesPsophocarpus tetragonolobus (winged bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsManoj, N. / Srinivas, V.R. / Surolia, A. / Vijayan, M. / Suguna, K.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Carbohydrate specificity and salt-bridge mediated conformational change in acidic winged bean agglutinin.
Authors: Manoj, N. / Srinivas, V.R. / Surolia, A. / Vijayan, M. / Suguna, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary Crystallographic Analysis of Winged Bean Acidic Lectin
Authors: Manoj, N. / Srinivas, V.R. / Satish, B. / Singha, N.C. / Suguna, K.
History
DepositionJul 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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.mon_nstd_flag / _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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACIDIC LECTIN
B: ACIDIC LECTIN
C: ACIDIC LECTIN
D: ACIDIC LECTIN
E: ACIDIC LECTIN
F: ACIDIC LECTIN
G: ACIDIC LECTIN
H: ACIDIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,98138
Polymers211,1218
Non-polymers4,86030
Water1,44180
1
A: ACIDIC LECTIN
B: ACIDIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,20710
Polymers52,7802
Non-polymers1,4278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ACIDIC LECTIN
D: ACIDIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,20710
Polymers52,7802
Non-polymers1,4278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: ACIDIC LECTIN
F: ACIDIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,20710
Polymers52,7802
Non-polymers1,4278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: ACIDIC LECTIN
H: ACIDIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3598
Polymers52,7802
Non-polymers5786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.530, 125.910, 138.790
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe biological assembly is a dimer

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
ACIDIC LECTIN / ACIDIC AGGLUTININ


Mass: 26390.123 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Details: WINGED BEAN, PSOPHOCARPUS TETRAGONOLOBUS, SEEDS / Source: (natural) Psophocarpus tetragonolobus (winged bean) / Organ: LEGUMINOUS SEEDS / References: GenBank: 6018681, UniProt: Q9SM56*PLUS

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Sugars , 2 types, 14 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.: 6
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: Sugar
ChemComp-AMG / methyl alpha-D-galactopyranoside / ALPHA-METHYL-D-GALACTOSIDE / methyl alpha-D-galactoside / methyl D-galactoside / methyl galactoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H14O6
IdentifierTypeProgram
DGalp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-methyl-galactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 96 molecules

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


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.77 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Crystals were grown by the hanging-drop method. The drops contained 5 microlitres of 15mg/ml protein, a 20-fold molar excess of methyl-alpha-d-galactose in phosphate buffer pH 7.2 and 2ml of ...Details: Crystals were grown by the hanging-drop method. The drops contained 5 microlitres of 15mg/ml protein, a 20-fold molar excess of methyl-alpha-d-galactose in phosphate buffer pH 7.2 and 2ml of 35%(w/v) PEG 4000. 1ml of 35%(w/v) PEG 4000 was used as the reservoir solution. , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Manoj, N., (1999) Acta Crystallogr., D55, 564.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
335 %(w/v)PEG40001drop
435 %(w/v)PEG40001reservoir
2sugar1dropin phosphate buffer(20-fold molar excess)

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 5, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→28 Å / Num. all: 32900 / Num. obs: 69174 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.12
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.42 / Num. unique all: 3300 / % possible all: 93.6
Reflection
*PLUS
Num. obs: 32900 / Num. measured all: 69174
Reflection shell
*PLUS
% possible obs: 93.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WINGED BEAN ACIDIC LECTIN (PDB CODE 1F9K)

1f9k


Resolution: 3.3→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 162723.17 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1596 5 %RANDOM
Rwork0.204 ---
obs0.204 31958 92.4 %-
all-31958 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.19 e/Å3
Displacement parametersBiso mean: 47.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20 Å2-1.18 Å2
2--9.68 Å20 Å2
3----6.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13925 0 288 80 14293
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.7
X-RAY DIFFRACTIONc_improper_angle_d1.02
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 244 4.7 %
Rwork0.303 4945 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CIS.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.303

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