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- PDB-1aif: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB FROM MOUSE -

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Basic information

Entry
Database: PDB / ID: 1aif
TitleANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB FROM MOUSE
Components
  • ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB (HEAVY CHAIN)
  • ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN / C REGION / V REGION
Function / homology
Function and homology information


opsonization / immunoglobulin complex, circulating / immunoglobulin receptor binding / phagocytosis, recognition / B cell differentiation / positive regulation of B cell activation / phagocytosis, engulfment / antigen binding / complement activation, classical pathway / B cell receptor signaling pathway ...opsonization / immunoglobulin complex, circulating / immunoglobulin receptor binding / phagocytosis, recognition / B cell differentiation / positive regulation of B cell activation / phagocytosis, engulfment / antigen binding / complement activation, classical pathway / B cell receptor signaling pathway / external side of plasma membrane / defense response to bacterium / innate immune response / extracellular region / plasma membrane
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin C1-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like domain / Immunoglobulin C1-set / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Immunoglobulin kappa constant / gb:1042226:
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsBan, N. / Escobar, C. / Hasel, K. / Day, J. / Greenwood, A. / McPherson, A.
Citation
Journal: FASEB J. / Year: 1995
Title: Structure of an anti-idiotypic Fab against feline peritonitis virus-neutralizing antibody and a comparison with the complexed Fab.
Authors: Ban, N. / Escobar, C. / Hasel, K.W. / Day, J. / Greenwood, A. / McPherson, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Crystal Structure of an Idiotype-Anti-Idiotype Fab Complex
Authors: Ban, N. / Escobar, C. / Garcia, R. / Hasel, K. / Day, J. / Greenwood, A. / McPherson, A.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Preliminary Crystallographic Study of a Complex between an Fab of a Monoclonal Feline Peritonitis Virus Neutralizing Antibody and its Anti-Idiotypic Fab
Authors: Ban, N. / Escobar, C. / Day, J. / Greenwood, A. / McPherson, A.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Characterization of Crystals of an Fab Fragment of a Murine Monoclonal Antibody
Authors: Ban, N. / Escobar, C. / Day, J. / Greenwood, A. / Larson, S. / McPherson, A.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 14, 1994-
Revision 1.0Feb 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB (LIGHT CHAIN)
H: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB (HEAVY CHAIN)
A: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB (LIGHT CHAIN)
B: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)94,7474
Polymers94,7474
Non-polymers00
Water0
1
L: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB (LIGHT CHAIN)
H: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,3742
Polymers47,3742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-24 kcal/mol
Surface area20510 Å2
MethodPISA
2
A: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB (LIGHT CHAIN)
B: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,3742
Polymers47,3742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-25 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)57.200, 71.200, 75.800
Angle α, β, γ (deg.)85.30, 121.40, 116.50
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB (LIGHT CHAIN)


Mass: 23560.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837
#2: Antibody ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB (HEAVY CHAIN)


Mass: 23812.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 1042226

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein solution1drop
20.015 Macetate1drop
38-10 %(w/v)PEG40001drop
416-20 %(w/v)PEG40001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionObserved criterion σ(I): 3
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / Num. obs: 18603 / % possible obs: 94 % / Num. measured all: 74745

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.9→20 Å / σ(F): 3 /
Rfactor% reflection
Rwork0.22 -
Obs0.22 83 %
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6662 0 0 0 6662
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
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_deg2.5
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
Refinement
*PLUS
Num. reflection obs: 16482
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg28.8
X-RAY DIFFRACTIONx_improper_angle_deg2.2

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