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- PDB-2dbl: MOLECULAR BASIS OF CROSS-REACTIVITY AND THE LIMITS OF ANTIBODY-AN... -

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Basic information

Entry
Database: PDB / ID: 2dbl
TitleMOLECULAR BASIS OF CROSS-REACTIVITY AND THE LIMITS OF ANTIBODY-ANTIGEN COMPLEMENTARITY
Components
  • IGG1-KAPPA DB3 FAB (HEAVY CHAIN)
  • IGG1-KAPPA DB3 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding ...phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / cytoplasm
Similarity search - Function
: / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...: / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
5-ALPHA-PREGNANE-3-BETA-OL-HEMISUCCINATE / : / Ig gamma-1 chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsArevalo, J.H. / Wilson, I.A.
Citation
Journal: Nature / Year: 1993
Title: Molecular basis of crossreactivity and the limits of antibody-antigen complementarity.
Authors: Arevalo, J.H. / Taussig, M.J. / Wilson, I.A.
#1: Journal: To be Published
Title: Structural Analysis of Antibody Specificity: Detailed Comparison of Five Fab'-Steroid Complexes
Authors: Arevalo, J.H. / Hassig, C.A. / Stura, E.A. / Taussig, M.J. / Wilson, I.A.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Three-Dimensional Structure of an Anti-Steroid Fab' and Progesterone-Fab' Complex
Authors: Arevalo, J.H. / Stura, E.A. / Taussig, M.J. / Wilson, I.A.
#3: Journal: Immunology / Year: 1987
Title: Analysis of an Anti-Progesterone Antibody: Variable Crystal Morphology of the Fab' and Steroid-Fab' Complexes
Authors: Stura, E.A. / Arevalo, J.H. / Feinstein, A. / Heap, R.B. / Taussig, M.J. / Wilson, I.A.
History
DepositionFeb 8, 1994Processing site: BNL
Revision 1.0Mar 7, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG1-KAPPA DB3 FAB (LIGHT CHAIN)
H: IGG1-KAPPA DB3 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0543
Polymers47,6352
Non-polymers4191
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-21 kcal/mol
Surface area19740 Å2
MethodPISA
2
L: IGG1-KAPPA DB3 FAB (LIGHT CHAIN)
H: IGG1-KAPPA DB3 FAB (HEAVY CHAIN)
hetero molecules

L: IGG1-KAPPA DB3 FAB (LIGHT CHAIN)
H: IGG1-KAPPA DB3 FAB (HEAVY CHAIN)
hetero molecules

L: IGG1-KAPPA DB3 FAB (LIGHT CHAIN)
H: IGG1-KAPPA DB3 FAB (HEAVY CHAIN)
hetero molecules

L: IGG1-KAPPA DB3 FAB (LIGHT CHAIN)
H: IGG1-KAPPA DB3 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,21512
Polymers190,5418
Non-polymers1,6744
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
crystal symmetry operation12_565x,x-y+1,-z+2/31
Buried area24140 Å2
ΔGint-107 kcal/mol
Surface area72260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.760, 134.760, 124.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO L 141 / 4: CIS PROLINE - PRO H 149 / 5: CIS PROLINE - PRO H 151 / 6: CIS PROLINE - PRO H 202

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Components

#1: Antibody IGG1-KAPPA DB3 FAB (LIGHT CHAIN)


Mass: 23880.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 1589925
#2: Antibody IGG1-KAPPA DB3 FAB (HEAVY CHAIN)


Mass: 23754.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01868
#3: Chemical ChemComp-S5H / 5-ALPHA-PREGNANE-3-BETA-OL-HEMISUCCINATE


Mass: 418.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H38O5
Has protein modificationY
Nonpolymer detailsTHE 5-ALPHA-PREGNANE-3-BETA-OL-HEMISUCCINATE MOLECULE (S5H) IS LOCATED BETWEEN THE COMPLEMENTARITY- ...THE 5-ALPHA-PREGNANE-3-BETA-OL-HEMISUCCINATE MOLECULE (S5H) IS LOCATED BETWEEN THE COMPLEMENTARITY-DETERMINING REGIONS L1, L3, H1, H2 AND H3.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 63.99 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7 Mammonium sulfate1reservoir
20.15 Mimidazole citrate1reservoir
30.002 %(w/v)PEG200001reservoir
41 %(v/v)ethanol1reservoir
55-10 mgFab1reservoir

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.9→6 Å / Rfactor Rwork: 0.205 / Rfactor obs: 0.205 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 30 0 3380
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg3.082
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
Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.082

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