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- PDB-1g7y: THE CRYSTAL STRUCTURE OF THE 58KD VEGETATIVE LECTIN FROM THE TROP... -

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Basic information

Entry
Database: PDB / ID: 1g7y
TitleTHE CRYSTAL STRUCTURE OF THE 58KD VEGETATIVE LECTIN FROM THE TROPICAL LEGUME DOLICHOS BIFLORUS
ComponentsSTEM/LEAF LECTIN DB58
KeywordsSUGAR BINDING PROTEIN / JELLY ROLL FOLD / LECTIN
Function / homology
Function and homology information


Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesVigna unguiculata subsp. cylindrica (catjang)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsButs, L. / Hamelryck, T.W. / Loris, R. / Dao-Thi, M.-H. / 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: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallisation of two related lectins from the legume plant Dolichos biflorus
Authors: Dao-Thi, M. / Hamelryck, T.W. / Bouckaert, J. / Koerber, F. / Burkow, V. / Poortmans, F. / Etzler, M. / Strecker, G. / Wyns, L. / Loris, R.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectins oligomers from Dolichos biflorus
Authors: Hamelryck, T.W. / Loris, R. / Bouckaert, J. / Dao-Thi, M.-H. / Strecker, G. / Imberty, A. / Fernandez, E. / Wyns, L. / Etzler, M.E.
History
DepositionNov 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 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 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 / diffrn_source / 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 / pdbx_struct_conn_angle / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STEM/LEAF LECTIN DB58
B: STEM/LEAF LECTIN DB58
C: STEM/LEAF LECTIN DB58
D: STEM/LEAF LECTIN DB58
E: STEM/LEAF LECTIN DB58
F: STEM/LEAF LECTIN DB58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,16321
Polymers162,8816
Non-polymers2,28215
Water73941
1
A: STEM/LEAF LECTIN DB58
B: STEM/LEAF LECTIN DB58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0547
Polymers54,2942
Non-polymers7615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: STEM/LEAF LECTIN DB58
D: STEM/LEAF LECTIN DB58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0547
Polymers54,2942
Non-polymers7615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: STEM/LEAF LECTIN DB58
F: STEM/LEAF LECTIN DB58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0547
Polymers54,2942
Non-polymers7615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.941, 130.272, 137.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
STEM/LEAF LECTIN DB58


Mass: 27146.885 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: TROPICAL LEGUME
Source: (natural) Vigna unguiculata subsp. cylindrica (catjang)
Species: Vigna unguiculata / Strain: subsp. cylindrica / References: UniProt: P19588

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Sugars , 2 types, 3 molecules

#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
#3: Polysaccharide beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...beta-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 53 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 5-7 mg/ml protein; 100mM sodium citrate; 8-12%(w/v) PEG(6000); 0.2-0.4M sodium chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.98089 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 20, 1998
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98089 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 276382 / Num. obs: 259246 / % possible obs: 93.8 % / Observed criterion σ(I): 5 / Redundancy: 4.4 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.9
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.78 / % possible all: 95.7
Reflection
*PLUS
Num. all: 259246 / Num. obs: 59075 / Num. measured all: 276382
Reflection shell
*PLUS
% possible obs: 95.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: non-canonical legume lectin dimer (non-canonical half of a DBL tetramer)

Resolution: 2.5→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2558709.98 / 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
Rfree0.247 5907 10.1 %RANDOM
Rwork0.221 ---
obs0.221 59071 93.6 %-
all-59071 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.12 Å2 / ksol: 0.289 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11044 0 126 41 11211
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it3.681.5
X-RAY DIFFRACTIONc_mcangle_it5.262
X-RAY DIFFRACTIONc_scbond_it6.412
X-RAY DIFFRACTIONc_scangle_it7.682.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 985 10 %
Rwork0.314 8856 -
obs--94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM.CIS_PEPTIDE
X-RAY DIFFRACTION4PARAM.METALSTOPOL.METALS
X-RAY DIFFRACTION5PARAM.CHO3TOPOL.CHO3
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.8 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_deg26.3
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: 0.359 / % reflection Rfree: 10 % / Rfactor Rwork: 0.314

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