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- PDB-1lof: X-RAY STRUCTURE OF A BIANTENNARY OCTASACCHARIDE-LECTIN COMPLEX AT... -

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Entry
Database: PDB / ID: 1lof
TitleX-RAY STRUCTURE OF A BIANTENNARY OCTASACCHARIDE-LECTIN COMPLEX AT 2.3 ANGSTROMS RESOLUTION
Components
  • (LEGUME ISOLECTIN I (ALPHA ...) x 2
  • (LEGUME ISOLECTIN I (BETA ...) x 2
KeywordsLECTIN
Function / homology
Function and homology information


D-mannose binding / metal ion binding
Similarity search - Function
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
: / Lectin beta-1 and beta-2 chains / Mannose/glucose-specific lectin alpha 1 chain
Similarity search - Component
Biological speciesLathyrus ochrus (yellow-flowered pea)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsBourne, Y. / Cambillau, C.
CitationJournal: J.Biol.Chem. / Year: 1992
Title: X-ray structure of a biantennary octasaccharide-lectin complex refined at 2.3-A resolution.
Authors: Bourne, Y. / Rouge, P. / Cambillau, C.
History
DepositionJan 27, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_database_status.process_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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: LEGUME ISOLECTIN I (ALPHA CHAIN)
B: LEGUME ISOLECTIN I (BETA CHAIN)
C: LEGUME ISOLECTIN I (ALPHA CHAIN)
D: LEGUME ISOLECTIN I (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,52110
Polymers51,3474
Non-polymers2,1746
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: LEGUME ISOLECTIN I (ALPHA CHAIN)
D: LEGUME ISOLECTIN I (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3575
Polymers25,7162
Non-polymers6413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-49 kcal/mol
Surface area9570 Å2
MethodPISA
3
A: LEGUME ISOLECTIN I (ALPHA CHAIN)
B: LEGUME ISOLECTIN I (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1645
Polymers25,6312
Non-polymers1,5333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10350 Å2
ΔGint-29 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.300, 75.400, 103.900
Angle α, β, γ (deg.)90.00, 92.00, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: ALA A 80 - ASP A 81 OMEGA = 353.52 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA C 80 - ASP C 81 OMEGA = 343.01 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

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LEGUME ISOLECTIN I (ALPHA ... , 2 types, 2 molecules AC

#1: Protein LEGUME ISOLECTIN I (ALPHA CHAIN)


Mass: 19847.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lathyrus ochrus (yellow-flowered pea) / Organ: SEED / References: UniProt: P04122
#3: Protein LEGUME ISOLECTIN I (ALPHA CHAIN)


Mass: 19905.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lathyrus ochrus (yellow-flowered pea) / Organ: SEED / References: UniProt: P04122

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LEGUME ISOLECTIN I (BETA ... , 2 types, 2 molecules BD

#2: Protein LEGUME ISOLECTIN I (BETA CHAIN)


Mass: 5783.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lathyrus ochrus (yellow-flowered pea) / Organ: SEED / References: UniProt: P12306
#4: Protein LEGUME ISOLECTIN I (BETA CHAIN)


Mass: 5810.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lathyrus ochrus (yellow-flowered pea) / Organ: SEED / References: UniProt: P12306

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Sugars , 2 types, 2 molecules

#5: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1438.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGalpb1-4DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-2-3-1-4-3-1-4/a4-b1_b3-c1_b6-f1_c2-d1_d4-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-1-2/a3-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 234 molecules

#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsONE CA++ AND MN++ ION PER MONOMER: CA A 227, MN A 228, CA C 457 AND MN C 458. THERE IS ONE COMPLETE ...ONE CA++ AND MN++ ION PER MONOMER: CA A 227, MN A 228, CA C 457 AND MN C 458. THERE IS ONE COMPLETE OCTASACCHARIDE IN MONOMER 1: RESIDUES 501 TO 508. DUE TO WEAK ELECTRON DENSITY, THE ONLY SACCHARIDE RESIDUES THAT HAVE BEEN FITTED IN MONOMER 2 ARE MAN 511, MAN 512 AND NAG 515.
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: LEC1_LATOC SWISS-PROT RESIDUE PDB ATOM RECORDS NAME NUMBER NAME CHAIN SEQ/INSERT CODE LYS 153 ALA A 153 PHE 41 TYR B 41 PHE 41 TYR D 41 SER 52 ASN D 52

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
22 mM1dropCaCl2
31.5 mMOCTA1drop
438 %MPD1reservoir
50.1 mMHEPES1reservoir
60.1 M1reservoirNaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 24277 / % possible obs: 92 % / Num. measured all: 71100 / Rmerge(I) obs: 0.076

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→8 Å / Rfactor Rwork: 0.19 / Rfactor obs: 0.19 / σ(F): 1
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3601 0 138 230 3969
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.46
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Num. reflection obs: 22459 / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.46

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