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- PDB-1ioa: ARCELIN-5, A LECTIN-LIKE DEFENSE PROTEIN FROM PHASEOLUS VULGARIS -

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Basic information

Entry
Database: PDB / ID: 1ioa
TitleARCELIN-5, A LECTIN-LIKE DEFENSE PROTEIN FROM PHASEOLUS VULGARIS
ComponentsARCELIN-5A
KeywordsLECTIN / LECTIN-LIKE PROTEINS / PLANT DEFENSE PROTEINS
Function / homology
Function and homology information


nutrient reservoir activity / defense response / toxin activity / carbohydrate binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectin domain / Legume lectin domain / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPhaseolus vulgaris (common bean)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsHamelryck, T. / Loris, R.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: Crystal structure of arcelin-5, a lectin-like defense protein from Phaseolus vulgaris
Authors: Hamelryck, T. / Poortmans, F. / Goossens, A. / Angenon, G. / Van Montagu, M. / Wyns, L. / Loris, R.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: The Crystallographic Structure of Phytohemagglutinin-L
Authors: Hamelryck, T.W. / Dao-Thi, M.H. / Poortmans, F. / Chrispeels, M.J. / Wyns, L. / Loris, R.
#2: Journal: Plant Cell / Year: 1991
Title: Lectins, Lectin Genes, and Their Role in Plant Defense
Authors: Chrispeels, M.J. / Raikhel, N.V.
History
DepositionOct 2, 1996Processing site: BNL
Revision 1.0Dec 23, 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 26, 2014Group: Other
Revision 1.4Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
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 / 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 / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: ARCELIN-5A
B: ARCELIN-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0654
Polymers53,9242
Non-polymers1,1412
Water00
1
B: ARCELIN-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5322
Polymers26,9621
Non-polymers5711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ARCELIN-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5322
Polymers26,9621
Non-polymers5711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.300, 94.500, 82.900
Angle α, β, γ (deg.)90.00, 94.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.984554, 0.011087, -0.174727), (-0.010773, -0.999938, -0.002748), (-0.174747, -0.000823, 0.984613)
Vector: 23.42398, 10.05245, -39.51922)

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Components

#1: Protein ARCELIN-5A / ARC5A


Mass: 26961.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (common bean) / Organ: SEED / Strain: G02771 / References: PIR: S51359, UniProt: Q42460*PLUS
#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.: 2
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)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15.0 mg/mlprotein1drop
220 %(w/v)PEG40001drop
30.2 M1drop(NH4)2SO4
520 %(w/v)PEG40001reservoir
60.2 M1reservoir(NH4)2SO4
4sodium acetate1drop
7sodium acetate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Feb 22, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 16994 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.085

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Processing

Software
NameClassification
MADNESdata collection
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing
RefinementResolution: 2.7→10 Å / σ(F): 0
RfactorNum. reflection
Rfree0.269 -
Rwork0.205 -
obs0.205 49954
Displacement parametersBiso mean: 16.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3595 0 76 0 3671
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg2.17
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.22
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.06
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.06

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