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- PDB-2pel: PEANUT LECTIN -

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Basic information

Entry
Database: PDB / ID: 2pel
TitlePEANUT LECTIN
ComponentsPEANUT LECTIN
KeywordsLECTIN (AGGLUTININ) / LEGUME LECTIN / OPEN QUATERNARY STRUCTURE / CARBOHYDRATE SPECIFICITY / PROTEIN CRYSTALLOGRAPHY / AGGLUTININ
Function / homology
Function and homology information


carbohydrate binding / metal ion 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 domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / 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
beta-lactose / alpha-lactose / : / Galactose-binding lectin
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsBanerjee, R. / Das, K. / Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Conformation, protein-carbohydrate interactions and a novel subunit association in the refined structure of peanut lectin-lactose complex.
Authors: Banerjee, R. / Das, K. / Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Crystal Structure of Peanut Lectin, a Protein with an Unusual Quaternary Structure
Authors: Banerjee, R. / Mande, S.C. / Ganesh, V. / Das, K. / Dhanaraj, V. / Mahanta, S.K. / Suguna, K. / Surolia, A. / Vijayan, M.
#2: Journal: FEBS Lett. / Year: 1983
Title: Preparation and Preliminary X-Ray Studies of Three Acidic Ph Crystal Forms of the Anti-T Lectin from Peanut (Arachis Hypogaea)
Authors: Salunke, D.M. / Khan, M.I. / Surolia, A. / Vijayan, M.
#3: Journal: J.Mol.Biol. / Year: 1982
Title: Crystallization and Preliminary X-Ray Studies of the Anti-T Lectin from Peanut (Arachis Hypogaea)
Authors: Salunke, D.M. / Khan, M.I. / Surolia, A. / Vijayan, M.
History
DepositionAug 23, 1995Processing site: BNL
SupersessionDec 7, 1996ID: 1PEL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
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 / pdbx_struct_conn_angle / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: PEANUT LECTIN
B: PEANUT LECTIN
C: PEANUT LECTIN
D: PEANUT LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,58516
Polymers100,8364
Non-polymers1,74912
Water10,142563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.300, 126.900, 76.900
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(-0.997, -0.073, -0.0275), (-0.0779, 0.951, 0.2994), (0.0043, 0.3006, -0.9537)63.7616, -7.4416, 64.6975
2given(0.4962, 0.2333, 0.8362), (-0.3564, -0.8236, 0.4413), (0.7917, -0.517, -0.3255)-33.0204, 0.6363, 7.8144
3given(-0.4627, -0.144, -0.8748), (-0.1461, -0.9608, 0.2355), (-0.8744, 0.2368, 0.4235)95.7783, -0.6894, 59.0523

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PEANUT LECTIN / PEANUT AGGLUTININ


Mass: 25208.955 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: P02872

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Sugars , 2 types, 4 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 571 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 57 %
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.6 %protein11
20.05 Msodium phosphate11
312 %(w/v)PEG600011

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.25 Å / Num. obs: 50764 / % possible obs: 88 % / Rmerge(I) obs: 0.079
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 173209
Reflection shell
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 2.34 Å / % possible obs: 42.3 % / Num. unique obs: 4508 / Num. measured obs: 7107 / Rmerge(I) obs: 0.15

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Processing

Software
NameClassification
PROLSQrefinement
XENGENdata reduction
RefinementResolution: 2.25→10 Å / σ(F): 3
Details: THERE IS A TETRAMER IN THE ASYMMETRIC UNIT WITHOUT 222 OR FOUR-FOLD SYMMETRY.
RfactorNum. reflection% reflection
Rwork0.164 --
obs-44510 78 %
Displacement parametersBiso mean: 22.45 Å2
Refine analyzeLuzzati coordinate error obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 2.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6972 0 100 563 7635
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1240.15
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.2120.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.180.3
X-RAY DIFFRACTIONp_planar_tor1.9143
X-RAY DIFFRACTIONp_staggered_tor15.83315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.8915
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.5 Å2

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