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Basic information

Entry
Database: PDB / ID: 1fat
TitlePHYTOHEMAGGLUTININ-L
ComponentsPHYTOHEMAGGLUTININ-L
KeywordsLECTIN / GLYCOPROTEIN / PLANT DEFENSE PROTEIN
Function / homology
Function and homology information


D-mannose binding / defense response / toxin activity
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
: / Leucoagglutinating phytohemagglutinin
Similarity search - Component
Biological speciesPhaseolus vulgaris (common bean)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsHamelryck, T. / Loris, R.
Citation
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.
#1: Journal: Proteins / Year: 1996
Title: Crystallization of Glycosylated and Nonglycosylated Phytohemagglutinin-L
Authors: Dao-Thi, M.H. / Hamelryck, T.W. / Poortmans, F. / Voelker, T.A. / Chrispeels, M.J. / Wyns, L.
#2: Journal: Plant Cell / Year: 1991
Title: Lectins, Lectin Genes, and Their Role in Plant Defense
Authors: Chrispeels, M.J. / Raikhel, N.V.
#3: Journal: Embo J. / Year: 1985
Title: Characterization of Two Phaseolus Vulgaris Phytohemagglutinin Genes Closely Linked on the Chromosome
Authors: Hoffman, L.M. / Donaldson, D.D.
History
DepositionJun 12, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 23, 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 ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHYTOHEMAGGLUTININ-L
B: PHYTOHEMAGGLUTININ-L
C: PHYTOHEMAGGLUTININ-L
D: PHYTOHEMAGGLUTININ-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,01816
Polymers109,7534
Non-polymers1,26512
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.300, 121.200, 90.800
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number5
Space group name H-MC121
DetailsPHYTOHEMAGGLUTININ-L IS A HOMOTETRAMER WITH 222 SYMMETRY. EACH SUBUNIT CONSISTS OF 252 RESIDUES. THE FOUR SUBUNITS HAVE CHAIN IDENTIFIERS A, B, C, AND D IN THIS ENTRY.

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Components

#1: Protein
PHYTOHEMAGGLUTININ-L / LEUCOAGGLUTINATING PHYTOHEMAGGLUTININ / PHA-L


Mass: 27438.260 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PURIFIED PHA-L WAS PURCHASED FROM SIGMA / Source: (natural) Phaseolus vulgaris (common bean) / Organ: SEED / References: UniProt: P05087
#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.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsPHYTOHEMAGGLUTININ-L IS A GLYCOPROTEIN. IT CONTAINS ONE HI MANNOSE TYPE AND ONE COMPLEX TYPE SUGAR ...PHYTOHEMAGGLUTININ-L IS A GLYCOPROTEIN. IT CONTAINS ONE HI MANNOSE TYPE AND ONE COMPLEX TYPE SUGAR PER MONOMER. ONLY GLCNAC RESIDUE OF THE MANNOSE TYPE SUGAR ATTACHED TO ASN 12 IS VISIBLE IN THE ELECTRON DENSITY. NO INTERPRETABLE DENSITY IS OBSERVED FOR THE COMPLEX TYPE SUGAR ATTACHED TO ASN 60. EACH MONOMER HAS A BOUND CALCIUM AND MANGANESE ATOM. THE CALCIUM AND MANGANESE IONS ARE ESSENTIAL FOR STABILIZING AN UNUSUAL ALA-ASP CIS PEPTIDE BOND THAT IS AN ESSENTIAL FEATURE OF THE CARBOHYDRATE RECOGNITION SITE OF THIS LECTIN. THESE SITES ARE PRESENTED ON *SITE* RECORDS BELOW.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 45.9 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 %(w/v)PEG60001reservoir
2100 mMTris1reservoir
38 %(w/v)PEG60001drop
4100 mMTris1drop
55 mg/mlPHA-L solution1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorDetector: AREA DETECTOR / Date: Jul 5, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 2.5 % / Biso Wilson estimate: 43.74 Å2 / Rmerge(I) obs: 0.099

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.8→10 Å / Cross valid method: A POSTERIORI R-FREE FACTOR / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2758 10 %RANDOM
Rwork0.2 ---
obs0.2 67416 88 %-
Displacement parametersBiso mean: 24.34 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 64 16 7248
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_deg2.01
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.16
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.71
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
Refine LS restraints NCSNCS model details: MONOMERS A, B, C, D / Weight Biso : 1 / Weight position: 300
LS refinement shellResolution: 2.8→2.94 Å
RfactorNum. reflection% reflection
Rfree0.28 299 10 %
Rwork0.29 1832 -
obs--81.8 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.16
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.71

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