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- PDB-1igi: 26-10 FAB:DIGOXIN COMPLEX-AFFINITY AND SPECIFICITY DUE TO SURFACE... -

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Basic information

Entry
Database: PDB / ID: 1igi
Title26-10 FAB:DIGOXIN COMPLEX-AFFINITY AND SPECIFICITY DUE TO SURFACE COMPLEMENTARITY
Components
  • IGG2A-KAPPA 26-10 FAB (HEAVY CHAIN)
  • IGG2A-KAPPA 26-10 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsJeffrey, P.D. / Sheriff, S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: 26-10 Fab-digoxin complex: affinity and specificity due to surface complementarity.
Authors: Jeffrey, P.D. / Strong, R.K. / Sieker, L.C. / Chang, C.Y. / Campbell, R.L. / Petsko, G.A. / Haber, E. / Margolies, M.N. / Sheriff, S.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Crystallization of the Fab Fragment of a Monoclonal Anti-Digoxin Antibody and its Complex with Digoxin
Authors: Rose, D.R. / Seaton, B.A. / Petsko, G.A. / Novotny, J. / Margolies, M.N. / Locke, E. / Haber, E.
History
DepositionFeb 19, 1993Processing site: BNL
Revision 1.0Apr 15, 1993Provider: 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
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
Revision 1.4Nov 6, 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: IGG2A-KAPPA 26-10 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA 26-10 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,3652
Polymers47,3652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-25 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.780, 89.250, 59.240
Angle α, β, γ (deg.)90.00, 95.94, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES 8, 95, 141 OF THE L CHAIN AND 149, 151, 200 OF THE H CHAIN ARE CIS PROLINES.

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Components

#1: Antibody IGG2A-KAPPA 26-10 FAB (LIGHT CHAIN)


Mass: 24057.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / References: PIR: S52028
#2: Antibody IGG2A-KAPPA 26-10 FAB (HEAVY CHAIN)


Mass: 23307.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / References: PIR: S38950
Has protein modificationY
Sequence detailsTHE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E.KABAT (E.A.KABAT,T.T.WU,H.M.PERRY,K.S. ...THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E.KABAT (E.A.KABAT,T.T.WU,H.M.PERRY,K.S.GOTTESMAN,C.FOELLER SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 5TH ED., (1991), NATIONAL INSTITUTES OF HEALTH,BETHESDA,MD.).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116-18 %(w/w)PEG800011
21.7 %(v/v)MPD11
310 mMsodium phosphate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 7998 / % possible obs: 61 % / Num. measured all: 16046 / Rmerge(I) obs: 0.056

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.7→8 Å / Rfactor Rwork: 0.177 / σ(F): 1
Details: THE FOLLOWING REGIONS OF THE HEAVY CHAIN (H) WERE INCLUDED IN THE MODEL BUT HAVE POORLY DEFINED ELECTRON DENSITY: 25 - 30, 53 - 56, AND 128 - 137.
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 0 0 3299
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg3.3
X-RAY DIFFRACTIONx_dihedral_angle_d28.3
X-RAY DIFFRACTIONx_improper_angle_d1.33
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 7326 / Rfactor Rwork: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.33

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