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- PDB-1jlx: AGGLUTININ IN COMPLEX WITH T-DISACCHARIDE -

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Basic information

Entry
Database: PDB / ID: 1jlx
TitleAGGLUTININ IN COMPLEX WITH T-DISACCHARIDE
ComponentsAGGLUTININ
KeywordsLECTIN / COMPLEX (LECTIN-SACCHARIDE) / T-DISACCHARIDE HOMODIMER / BIVALENT
Function / homology
Function and homology information


Agglutinin domain / Agglutinin domain superfamily / Agglutinin domain / Agglutinin / : / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Thomsen-Friedenreich antigen / FORMYL GROUP / TOLUENE / : / Agglutinin
Similarity search - Component
Biological speciesAmaranthus caudatus (amaranth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTransue, T.R. / Smith, A.K. / Mo, H. / Goldstein, I.J. / Saper, M.A.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of benzyl T-antigen disaccharide bound to Amaranthus caudatus agglutinin.
Authors: Transue, T.R. / Smith, A.K. / Mo, H. / Goldstein, I.J. / Saper, M.A.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Isolation and Characterization of Amaranthin, a Lectin Present in the Seeds of Amaranthus Caudatus, that Recognizes the T-(or Cryptic T)-Antigen
Authors: Rinderle, S.J. / Goldstein, I.J. / Matta, K.L. / Ratcliffe, R.M.
History
DepositionJul 23, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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 2.1Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGGLUTININ
B: AGGLUTININ
A: FORMYL GROUP
B: FORMYL GROUP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6368
Polymers69,6252
Non-polymers1,0116
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint11 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.300, 99.200, 66.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.84, -0.543, -0.001), (-0.543, 0.84, 0.004), (-0.001, 0.004, -1)148.91701, 43.945, -3.597
2given(-0.856, -0.517, -0.015), (-0.518, 0.855, 0.017), (0.003, 0.023, -1)147.084, 41.684, -5.652

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Components

#1: Protein AGGLUTININ / AMARANTHIN / ACA


Mass: 34812.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Amaranthus caudatus (amaranth) / Organ: SEED / References: PIR: S24263, UniProt: Q71QF2*PLUS
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 383.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Thomsen-Friedenreich antigen
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O
#4: Chemical ChemComp-MBN / TOLUENE


Mass: 92.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE WAS DEDUCED FROM THE KNOWN SEQUENCE OF AN APPARENT HOMOLOGUE FROM AMARANTHUS ...THE SEQUENCE WAS DEDUCED FROM THE KNOWN SEQUENCE OF AN APPARENT HOMOLOGUE FROM AMARANTHUS HYPOCHONDRIACUS (PIR 99583, 423770) REPORTED AS A "SEED SPECIFIC PROTEIN OF BALANCED NUTRITIONAL QUALITY" (RAINA,A. AND DATTA,A., PROC. NATL. ACAD. SCI. U.S.A. 89, 11774-11778 (1992)), PARTIAL SEQUENCES OF PEPTIDE FRAGMENTS DERIVED FROM THE AMARANTHUS CAUDATUS PROTEIN BY PROTEOLYSIS, AND THE EXPERIMENTAL ELECTRON DENSITY. IT IS ALSO PROBABLE THAT IN SOME (AS YET UNIDENTIFIED) POSITIONS, MORE THAN ONE RESIDUE TYPE CONTRIBUTES TO THE ELECTRON DENSITY. ONLY ONE RESIDUE TYPE PER POSITION HAS BEEN MODELLED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 57 %
Crystal growpH: 6.7 / Details: pH 6.7
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
20.01 %sodium azide1drop
355 mMHEPES1drop
415 %PEG4001drop
530 %PEG4001reservoir
6100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorDetector: CCD / Date: Aug 7, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionNum. obs: 33071 / % possible obs: 88.4 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.3
Reflection shellHighest resolution: 2.2 Å / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 7.4

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JLY

1jly


Resolution: 2.2→10 Å / σ(F): 0
Details: THE N-TERMINAL ALA 1 APPEARS TO HAVE DENSITY CONSISTENT WITH A FORMYL GROUP ATTACHED TO THE N-TERMINUS.
RfactorNum. reflection% reflection
Rwork0.196 --
obs0.196 32663 88.4 %
Displacement parametersBiso mean: 23.06 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 66 297 5221
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.97
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.318
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3PARAM4.CHOTOPH4.CHO
X-RAY DIFFRACTION4TOPH01.FML
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.97
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.318

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