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- PDB-1jly: CRYSTAL STRUCTURE OF AMARANTHUS CAUDATUS AGGLUTININ -

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Basic information

Entry
Database: PDB / ID: 1jly
TitleCRYSTAL STRUCTURE OF AMARANTHUS CAUDATUS AGGLUTININ
ComponentsAGGLUTININ
KeywordsLECTIN / AGGLUTININ / 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
Biological speciesAmaranthus caudatus (amaranth)
MethodX-RAY DIFFRACTION / MIR / 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 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 20, 2013Group: Derived calculations
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGGLUTININ
B: AGGLUTININ


Theoretical massNumber of molelcules
Total (without water)69,6492
Polymers69,6492
Non-polymers00
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-13 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.300, 99.100, 66.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.839, -0.544), (-0.544, 0.839, 0.003), (-0.001, 0.002, -1)
Vector: 148.875, 44.017, -3.362)

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Components

#1: Protein AGGLUTININ / AMARANTHIN / ACA


Mass: 34824.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Amaranthus caudatus (amaranth) / Organ: SEED / References: UniProt: Q71QF2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 1

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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: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ADSC / Detector: AREA DETECTOR / Date: Mar 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 36419 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.3
Reflection shellHighest resolution: 2.2 Å / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 2.6 / % possible all: 72.2
Reflection
*PLUS
Highest resolution: 2.2 Å
Reflection shell
*PLUS
% possible obs: 72.2 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLORmodel building
X-PLORrefinement
SDMS(NIELSEN)data reduction
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR / 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
Rfree0.246 3641 10 %
Rwork0.174 --
obs0.174 32778 -
Displacement parametersBiso mean: 18.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4856 0 0 332 5188
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_d27.15
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.343
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 DIFFRACTION3TOPH01.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_deg27.15
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.343

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