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- PDB-1led: STRUCTURES OF THE LECTIN IV OF GRIFFONIA SIMPLICIFOLIA AND ITS CO... -

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Database: PDB / ID: 1led
TitleSTRUCTURES OF THE LECTIN IV OF GRIFFONIA SIMPLICIFOLIA AND ITS COMPLEX WITH THE LEWIS B HUMAN BLOOD GROUP DETERMINANT AT 2.0 ANGSTROMS RESOLUTION
ComponentsWEST-CENTRAL AFRICAN LEGUME LECTIN IV
KeywordsLECTIN
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, 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 speciesGriffonia simplicifolia (plant)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsDelbaere, L. / Vandonselaar, M. / Quail, J.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Structures of the lectin IV of Griffonia simplicifolia and its complex with the Lewis b human blood group determinant at 2.0 A resolution.
Authors: Delbaere, L.T. / Vandonselaar, M. / Prasad, L. / Quail, J.W. / Wilson, K.S. / Dauter, Z.
#1: Journal: Can.J.Chem. / Year: 1990
Title: Molecular Recognition of a Human Blood Group Determinant by a Plant Lectin
Authors: Delbaere, L.T.J. / Vandonselaar, M. / Prasad, L. / Quail, J.W. / Pearlstone, J.R. / Carpenter, M.R. / Smillie, L.B. / Nikrad, P.V. / Spohr, U. / Lemieux, R.U.
#2: Journal: Trans.Am.Crystallogr.Assoc. / Year: 1991
Title: Structures of Griffonia Simplicifolia Lectin Iv and its Complex with a Synthetic Lewis B Blood Group Determinant
Authors: Delbaere, L.T.J. / Vandonselaar, M. / Prasad, L. / Quail, J.W. / Nikrad, P.V. / Pearlstone, J.R. / Carpenter, M.R. / Smillie, L.B. / Spohr, U. / Lemieux, R.U.
History
DepositionDec 17, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Dec 25, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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_label_asym_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 / _pdbx_struct_special_symmetry.label_asym_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
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: WEST-CENTRAL AFRICAN LEGUME LECTIN IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2686
Polymers26,8171
Non-polymers1,4515
Water2,594144
1
A: WEST-CENTRAL AFRICAN LEGUME LECTIN IV
hetero molecules

A: WEST-CENTRAL AFRICAN LEGUME LECTIN IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,53612
Polymers53,6332
Non-polymers2,90310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)78.900, 78.900, 89.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Atom site foot note1: RESIDUE PRO 86 IS A CIS PROLINE.
2: PEPTIDE BONDS ALA 88 - ASP 89 AND VAL 221 - GLY 222 ARE CIS PEPTIDE BONDS AND ARE INVOLVED IN CARBOHYDRATE BINDING SITE.
3: WATERS 403 AND 404 OCCUPY SPECIAL POSITIONS AND ARE SHARED BY TWO SYMMETRY RELATED MOLECULES.
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-404-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein WEST-CENTRAL AFRICAN LEGUME LECTIN IV


Mass: 26816.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Griffonia simplicifolia (plant) / References: UniProt: P24146

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]methyl 2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 689.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3[LFucpa1-4]DGlcpNAc[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_1*OC_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3-3/a3-b1_a4-d1_b2-c1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}[(4+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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.: 1
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

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Non-polymers , 4 types, 147 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Details: Vandonselaar,M., (1987) J. Biol. Chem., 262, 10848.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-6 mg/mlprotein1drop
218-20 %satammonium sulfate1drop
350 mMPIPES1droppH6.2
40.01 %sodium azide1drop
52.2 mol/mollectin1dropetrasaccharide
636-40 %satammonium sulfate1reservoir
70.1 MPIPES1reservoir
80.02 %sodium azide1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementHighest resolution: 2 Å
Details: RESIDUES 1 AND 241 - 243 HAVE VERY HIGH TEMPERATURE FACTORS AND ARE NOT WELL DETERMINED.
RfactorNum. reflection
obs0.181 19212
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 92 144 2140
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d3.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Rfactor all: 0.181 / Num. reflection obs: 19212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d3.02
X-RAY DIFFRACTIONp_angle_deg3.02

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