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- PDB-1wbf: WINGED BEAN LECTIN, SACCHARIDE FREE FORM -

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Basic information

Entry
Database: PDB / ID: 1wbf
TitleWINGED BEAN LECTIN, SACCHARIDE FREE FORM
ComponentsPROTEIN (AGGLUTININ)
KeywordsSUGAR BINDING PROTEIN / LECTIN (AGGLUTININ) / LEGUME LECTIN / PROTEIN CRYSTALLOGRAPHY / BLOOD GROUP SPECIFICITY / SACCHARIDE FREE FORM
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
: / Basic agglutinin
Similarity search - Component
Biological speciesPsophocarpus tetragonolobus (winged bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsManoj, N. / Srinivas, V.R. / Suguna, K.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structure of basic winged-bean lectin and a comparison with its saccharide-bound form.
Authors: Manoj, N. / Srinivas, V.R. / Suguna, K.
#1: 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.
#2: 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
DepositionDec 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.conn_type_id / _struct_conn.id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 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
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (AGGLUTININ)
B: PROTEIN (AGGLUTININ)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,34810
Polymers53,2742
Non-polymers1,0758
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.159, 75.161, 95.772
Angle α, β, γ (deg.)90.00, 106.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-679-

HOH

21B-730-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8291, -0.006, 0.559), (-0.0007, -1, -0.0098), (0.5591, 0.0077, -0.8291)
Vector: -13.6814, 34.5292, 45.2376)

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Components

#1: Protein PROTEIN (AGGLUTININ) / WINGED BEAN BASIC AGGLUTININ


Mass: 26636.799 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Psophocarpus tetragonolobus (winged bean) / References: UniProt: O24313
#2: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
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: 3.26 Å3/Da / Density % sol: 61.1 %
Crystal growpH: 7
Details: CRYSTALS WERE GROWN BY BATCH 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 AZIDE, ...Details: CRYSTALS WERE GROWN BY BATCH 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 AZIDE, WAS MIXED WITH 45% MPD IN THE SAME BUFFER AT 20 DEGREES CENTIGRADE.
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein11
20.02 Mphosphate11
30.15 M11NaCl
40.025 %(w/v)11NaN3
56-7.5 %(w/v)PEG400011
70.02 Mphosphate1reservoir
840 %PEG40001reservoir
6sugar1120 times molar excess

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→29.6 Å / Num. obs: 26671 / % possible obs: 88.7 % / Redundancy: 1.5 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.5
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.8 / % possible all: 80.6
Reflection
*PLUS
Num. measured all: 38947
Reflection shell
*PLUS
% possible obs: 80.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WBL

1wbl


Resolution: 2.3→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1870 8 %RANDOM
Rwork0.197 ---
obs-23516 80.3 %-
Displacement parametersBiso mean: 31.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 60 283 3965
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
X-RAY DIFFRACTIONx_improper_angle_d1.45
X-RAY DIFFRACTIONx_mcbond_it2.991.5
X-RAY DIFFRACTIONx_mcangle_it4.492
X-RAY DIFFRACTIONx_scbond_it4.972
X-RAY DIFFRACTIONx_scangle_it6.482.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 307 8.3 %
Rwork0.286 3402 -
obs--76.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM1.CHOTOPH1.CHO
X-RAY DIFFRACTION3PARAM11.WATTOPH19.PEP
X-RAY DIFFRACTION4PARAM19.IONTOPH11.WAT
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_deg27.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.45

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