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

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Basic information

Entry
Database: PDB / ID: 1igj
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 / DIGOXIN / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.5 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.
#2: Journal: Acta Crystallogr.,Sect.A / Year: 1991
Title: Solution of a Fab (26-10)Digoxin Complex by Generalized Molecular Replacement
Authors: Brunger, A.T.
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 / 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 16, 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

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Assembly

Deposited unit
A: IGG2A-KAPPA 26-10 FAB (LIGHT CHAIN)
B: IGG2A-KAPPA 26-10 FAB (HEAVY CHAIN)
C: IGG2A-KAPPA 26-10 FAB (LIGHT CHAIN)
D: IGG2A-KAPPA 26-10 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2916
Polymers94,7294
Non-polymers1,5622
Water00
1
A: IGG2A-KAPPA 26-10 FAB (LIGHT CHAIN)
B: IGG2A-KAPPA 26-10 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1463
Polymers47,3652
Non-polymers7811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-27 kcal/mol
Surface area19050 Å2
MethodPISA
2
C: IGG2A-KAPPA 26-10 FAB (LIGHT CHAIN)
D: IGG2A-KAPPA 26-10 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1463
Polymers47,3652
Non-polymers7811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-29 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.160, 164.430, 70.010
Angle α, β, γ (deg.)90.00, 108.37, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES 8, 95, 141 OF THE A AND C CHAINS AND 149, 151, 200 OF THE B AND D CHAINS ARE CIS PROLINES.

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Components

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


Mass: 24057.676 Da / Num. of mol.: 2
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / References: PIR: S38950
#3: Chemical ChemComp-DGX / DIGOXIN


Mass: 780.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H64O14 / Comment: medication*YM
Has protein modificationY
Nonpolymer detailsDIGOXIN IS DIGOXIGENIN TRIDIGITOXOSIDE, HOWEVER, THERE IS NO ELECTRON DENSITY FOR THE OUTERMOST TWO ...DIGOXIN IS DIGOXIGENIN TRIDIGITOXOSIDE, HOWEVER, THERE IS NO ELECTRON DENSITY FOR THE OUTERMOST TWO DIGITOXOSES IN BOTH COMPLEXES.
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: 2.55 Å3/Da / Density % sol: 51.67 %
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: 2.5 Å / Num. obs: 27121 / Num. measured all: 68345 / Rmerge(I) obs: 0.048

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.5→8 Å / Rfactor Rwork: 0.176 / σ(F): 1
Details: CRYSTALS ARE TWINNED BY HEMI-MEROHEDRY SUCH THAT (H,K,L) REFLECTIONS FROM ONE LATTICE AND (H,K,-H-L) REFLECTIONS FROM THE OTHER LATTICE ARE SPATIALLY OVERLAPPED. TWIN FRACTION FOR CRYSTAL ...Details: CRYSTALS ARE TWINNED BY HEMI-MEROHEDRY SUCH THAT (H,K,L) REFLECTIONS FROM ONE LATTICE AND (H,K,-H-L) REFLECTIONS FROM THE OTHER LATTICE ARE SPATIALLY OVERLAPPED. TWIN FRACTION FOR CRYSTAL WHOSE DATA THE MODEL WAS REFINED AGAINST WAS ESTIMATED AT 43%. THE FOLLOWING REGIONS OF THE HEAVY CHAINS (B AND D) WERE INCLUDED IN THE MODEL BUT HAVE POORLY DEFINED ELECTRON DENSITY: 25 - 31, 53 - 56, AND 127 - 137.
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 74 0 6652
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_dihedral_angle_d28.1
X-RAY DIFFRACTIONx_improper_angle_d1.39
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 25135 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39

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