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- PDB-1g8w: IMPROVED STRUCTURE OF PHYTOHEMAGGLUTININ-L FROM THE KIDNEY BEAN -

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Basic information

Entry
Database: PDB / ID: 1g8w
TitleIMPROVED STRUCTURE OF PHYTOHEMAGGLUTININ-L FROM THE KIDNEY BEAN
ComponentsLEUCOAGGLUTINATING PHYTOHEMAGGLUTININ
KeywordsSUGAR BINDING PROTEIN / JELLY-ROLL FOLD / LEGUME LECTIN
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsButs, L. / Hamelryck, T.W. / Dao-Thi, M. / Loris, R. / Wyns, L. / Etzler, M.E.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Weak protein-protein interactions in lectins: the crystal structure of a vegetative lectin from the legume Dolichos biflorus.
Authors: Buts, L. / Dao-Thi, M.H. / Loris, R. / Wyns, L. / Etzler, M. / Hamelryck, T.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: The crystallographic structure of phytohemagglutinin-L
Authors: Hamelryck, T.W. / Dao-Thi, M. / Poortmans, F. / Chrispeels, M.J. / Wyns, L. / Loris, R.
#2: Journal: Proteins / Year: 1996
Title: Crystallisation of glycosylated and non-glycosylated phytohemagglutinin-L
Authors: Dao-Thi, M. / Hamelryck, T.W. / Poortmans, F. / Voelker, T.A. / Chrispeels, M.J. / Wyns, L.
History
DepositionNov 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / 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.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 1.6Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEUCOAGGLUTINATING PHYTOHEMAGGLUTININ
B: LEUCOAGGLUTINATING PHYTOHEMAGGLUTININ
C: LEUCOAGGLUTINATING PHYTOHEMAGGLUTININ
D: LEUCOAGGLUTINATING PHYTOHEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,85716
Polymers101,5924
Non-polymers1,26512
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-81 kcal/mol
Surface area33680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.479, 121.278, 89.957
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
LEUCOAGGLUTINATING PHYTOHEMAGGLUTININ


Mass: 25397.959 Da / Num. of mol.: 4 / Fragment: LEUCOAGGLUTINATING FRACTION OF THE SEED LECTIN / Source method: isolated from a natural source / 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

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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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5 mg/ml protein; 100 mM TRIS/HCl; 8% (w/v) PEG(6000), pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-7 mg/mlprotein1reservoir
2100 mMsodium citrate1reservoir
38-12 %(w/v)PEG60001reservoir
40.2-0.4 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Aug 1, 1995
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→10 Å / Num. all: 105939 / Num. obs: 100006 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 3.8 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 11.23
Reflection shellResolution: 2.8→2.95 Å / Mean I/σ(I) obs: 3.2 / % possible all: 82.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. all: 100006 / Num. obs: 26546 / Num. measured all: 105939
Reflection shell
*PLUS
% possible obs: 82.1 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MADNESSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LES (lentil lectin)

1les


Resolution: 2.8→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3547881.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2509 9.9 %RANDOM
Rwork0.181 ---
all0.181 25349 --
obs0.181 25349 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.88 Å2 / ksol: 0.262 e/Å3
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.48 Å20 Å27.56 Å2
2--6.6 Å20 Å2
3----4.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7112 0 64 16 7192
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it3.231.5
X-RAY DIFFRACTIONc_mcangle_it5.12
X-RAY DIFFRACTIONc_scbond_it5.152
X-RAY DIFFRACTIONc_scangle_it6.992.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 264 9.9 %
Rwork0.28 2395 -
obs--57.2 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.31 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.28

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