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- PDB-1wbl: WINGED BEAN LECTIN COMPLEXED WITH METHYL-ALPHA-D-GALACTOSE -

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Basic information

Entry
Database: PDB / ID: 1wbl
TitleWINGED BEAN LECTIN COMPLEXED WITH METHYL-ALPHA-D-GALACTOSE
ComponentsWINGED BEAN LECTIN
KeywordsLECTIN / LEGUME LECTIN / GLYCOSYLATED PROTEIN / BLOOD GROUP SPECIFICITY / QUATERNARY ASSOCIATION / AGGLUTININ
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Legume lectin / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
methyl alpha-D-galactopyranoside / : / Basic agglutinin
Similarity search - Component
Biological speciesPsophocarpus tetragonolobus (winged bean)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsPrabu, M.M. / Sankaranarayanan, R. / Puri, K.D. / Sharma, V. / Surolia, A. / Vijayan, M. / Suguna, K.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Carbohydrate specificity and quaternary association in basic winged bean lectin: X-ray analysis of the lectin at 2.5 A resolution.
Authors: Prabu, M.M. / Sankaranarayanan, R. / Puri, K.D. / Sharma, V. / Surolia, A. / Vijayan, M. / Suguna, K.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Studies of the Basic Lectin from Winged Bean (Psophocarpus Tetragonolobus)
Authors: Sankaranarayanan, R. / Puri, K.D. / Ganesh, V. / Banerjee, R. / Surolia, A. / Vijayan, M.
History
DepositionApr 4, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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 / database_PDB_caveat / 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_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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_database_status.process_site / _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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn_type.id
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
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
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_seq_id / _atom_site.label_asym_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WINGED BEAN LECTIN
B: WINGED BEAN LECTIN
C: WINGED BEAN LECTIN
D: WINGED BEAN LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,88123
Polymers106,0224
Non-polymers4,85819
Water9,836546
1
A: WINGED BEAN LECTIN
B: WINGED BEAN LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,57912
Polymers53,0112
Non-polymers2,56810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: WINGED BEAN LECTIN
D: WINGED BEAN LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,30111
Polymers53,0112
Non-polymers2,2909
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.585, 91.908, 73.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.0862, -0.773, 0.6285), (-0.8088, -0.4227, -0.4088), (0.5817, -0.4731, -0.6617)95.9641, 117.4072, -18.6252
2given(-0.7144, 0.6857, -0.1395), (0.6856, 0.6461, -0.3353), (-0.1398, -0.3352, -0.9317)154.5275, -52.0396, 60.9444
3given(-0.6795, 0.3288, -0.6559), (-0.664, -0.656, 0.3589), (-0.3122, 0.6793, 0.6641)167.5327, 97.4342, 29.0241

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
WINGED BEAN LECTIN / WINGED BEAN BASIC AGGLUTININ


Mass: 26505.604 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Psophocarpus tetragonolobus (winged bean) / References: UniProt: O24313

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Sugars , 3 types, 11 molecules

#2: Polysaccharide
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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.: 2
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
#4: 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.: 4 / 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, 554 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: CRYSTALS WERE GROWN BY SITTING DROP METHOD IN WHICH 25 MICROLITERS OF AN 80 MG/ML PROTEIN SOLUTION IN 0.02M PHOSPHATE BUFFER AT PH 7.0, CONTAINING 0.15M SODIUM CHLORIDE, 0.025 (W/V) SODIUM ...Details: CRYSTALS WERE GROWN BY SITTING DROP METHOD IN WHICH 25 MICROLITERS OF AN 80 MG/ML PROTEIN SOLUTION IN 0.02M PHOSPHATE BUFFER AT PH 7.0, CONTAINING 0.15M SODIUM CHLORIDE, 0.025 (W/V) SODIUM NITRITE, 20 TIMES MOLAR EXCESS OF METHYL-ALPHA-D-GALACTOSE AND 6 TO 7.5% (W/V) PEG8000 WAS EQUILIBRATED AT 20 DEGREE CENTIGRADE WITH A RESERVOIR SOLUTION OF 40% PEG8000 IN THE SAME BUFFER., vapor diffusion - sitting drop
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
180 mg/mlprotein1drop
20.02 Mphosphate1drop
30.15 M1dropNaCl
40.025 %(w/v)1dropNaN3
520 Mmethyl-alpha-D-galactopyranoside1drop
66-7.5 %(w/v)PEG80001drop
740 %PEG80001reservoir
80.02 Mphosphate1reservoir
90.15 M1reservoirNaCl
100.025 %(w/v)1reservoirNaN3
1120 Mmethyl-alpha-D-galactopyranoside1reservoir

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Data collection

DiffractionMean temperature: 293 K
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1992
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.43→12.63 Å / Num. obs: 29837 / % possible obs: 77.3 % / Redundancy: 2.24 % / Biso Wilson estimate: 26.01 Å2 / Rmerge(I) obs: 0.064
Reflection shellResolution: 2.49→2.65 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.215 / % possible all: 40
Reflection
*PLUS
Num. measured all: 50842
Reflection shell
*PLUS
% possible obs: 39.8 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementStarting model: ERYTHRINA CORALLODENDRON LECTIN (FOR MOLECULAR REPLACEMENT)

Resolution: 2.5→100 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1373 5 %RANDOM
Rwork0.187 ---
obs0.187 29837 77.3 %-
Displacement parametersBiso mean: 21.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7287 0 306 546 8139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.65 Å
RfactorNum. reflection% reflection
Rfree0.4712 90 5.5 %
Rwork0.3459 1636 -
obs--39.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM1.CHOTOPH1.CHO
X-RAY DIFFRACTION3TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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