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- PDB-1jot: STRUCTURE OF THE LECTIN MPA COMPLEXED WITH T-ANTIGEN DISACCHARIDE -

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Basic information

Entry
Database: PDB / ID: 1jot
TitleSTRUCTURE OF THE LECTIN MPA COMPLEXED WITH T-ANTIGEN DISACCHARIDE
Components(AGGLUTININ) x 2
KeywordsLECTIN / MULTI-WAVELENGTH ANOMALOUS DIFFRACTION (MAD) / T-ANTIGEN / MACLURA POMIFERA / BETA PRISM
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Thomsen-Friedenreich antigen / Agglutinin alpha chain / Agglutinin beta-2 chain
Similarity search - Component
Biological speciesMaclura pomifera (Osage orange)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLee, X. / Thompson, A. / Zhang, Z. / Hoa, T.-T. / Biesterfeldt, J. / Ogata, C. / Xu, L. / Johnston, R.A.Z. / Young, N.M.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Structure of the complex of Maclura pomifera agglutinin and the T-antigen disaccharide, Galbeta1,3GalNAc.
Authors: Lee, X. / Thompson, A. / Zhang, Z. / Ton-that, H. / Biesterfeldt, J. / Ogata, C. / Xu, L. / Johnston, R.A. / Young, N.M.
History
DepositionDec 5, 1997Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
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 / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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 / _pdbx_struct_assembly_gen.asym_id_list / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 7, 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
Revision 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGGLUTININ
B: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2963
Polymers16,9132
Non-polymers3831
Water1,63991
1
A: AGGLUTININ
B: AGGLUTININ
hetero molecules

A: AGGLUTININ
B: AGGLUTININ
hetero molecules

A: AGGLUTININ
B: AGGLUTININ
hetero molecules

A: AGGLUTININ
B: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,18512
Polymers67,6528
Non-polymers1,5334
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area15850 Å2
ΔGint-51 kcal/mol
Surface area23530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.600, 67.600, 149.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein AGGLUTININ


Mass: 14768.595 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM THE SEEDS OF THE MORACEAE PLANT FAMILY / Source: (natural) Maclura pomifera (Osage orange) / Organ: SEEDS / References: UniProt: P18674
#2: Protein/peptide AGGLUTININ


Mass: 2144.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM THE SEEDS OF THE MORACEAE PLANT FAMILY / Source: (natural) Maclura pomifera (Osage orange) / Organ: SEEDS / References: UniProt: P18676
#3: 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.: 1
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.83 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.5
Details: CONVENTIONAL VAPOR DIFFUSION OF SITTING DROP. 1.0M OF LITHIUM SULFATE BUFFERED WITH 0.2 SODIUM CITRATE AT PH4.5 IN RESERVOIR DROPS MADE OF 15 MICROLITERS OF PROTEIN SOLUTION (10.0 MG/ML) AND ...Details: CONVENTIONAL VAPOR DIFFUSION OF SITTING DROP. 1.0M OF LITHIUM SULFATE BUFFERED WITH 0.2 SODIUM CITRATE AT PH4.5 IN RESERVOIR DROPS MADE OF 15 MICROLITERS OF PROTEIN SOLUTION (10.0 MG/ML) AND EQUAL VOLUMN OF RESERVOIR SOLUTION. ROOM TEMPERATURE., vapor diffusion - sitting drop
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5434
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 1, 1991
RadiationMonochromator: YES / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5434 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 10135 / % possible obs: 93.9999 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 7.84
Reflection shellResolution: 2.2→3.99 Å
Reflection
*PLUS
% possible obs: 93.5 % / Num. measured all: 98232

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Processing

Software
NameVersionClassification
X-PLOR3.85model building
X-PLOR3.85refinement
SOFTWARECAME WITH THE DETECTORdata reduction
HAMLINdata scaling
X-PLOR3.85phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OBTAINED FROM MAD

Resolution: 2.2→6 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.222 516 7.5 %YES
Rwork0.172 ---
obs0.172 9636 93.9 %-
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 26 91 1283
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.302
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.34
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.656
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
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rfree0.291 45
Rwork0.236 1006
Software
*PLUS
Name: X-PLOR / Version: 3.854 / 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_deg29.34
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.656
LS refinement shell
*PLUS
Rfactor obs: 0.236

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