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- PDB-1cic: IDIOTOPE-ANTI-IDIOTOPE FAB-FAB COMPLEX; D1.3-E225 -

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Basic information

Entry
Database: PDB / ID: 1cic
TitleIDIOTOPE-ANTI-IDIOTOPE FAB-FAB COMPLEX; D1.3-E225
Components(PROTEIN (IG HEAVY CHAIN V REGIONS)) x 4
KeywordsIMMUNOGLOBULIN / FAB COMPLEX / IDIOTOPE / ANTI-IDIOTOPE
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / blood microparticle / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Igk protein / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 2B / Ig gamma-1 chain C region, membrane-bound form / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBentley, G.A.
CitationJournal: Nature / Year: 1990
Title: Three-dimensional structure of an idiotope-anti-idiotope complex.
Authors: Bentley, G.A. / Boulot, G. / Riottot, M.M. / Poljak, R.J.
History
DepositionMar 31, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (IG HEAVY CHAIN V REGIONS)
B: PROTEIN (IG HEAVY CHAIN V REGIONS)
C: PROTEIN (IG HEAVY CHAIN V REGIONS)
D: PROTEIN (IG HEAVY CHAIN V REGIONS)


Theoretical massNumber of molelcules
Total (without water)93,9954
Polymers93,9954
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.110, 77.650, 96.750
Angle α, β, γ (deg.)90.00, 111.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody PROTEIN (IG HEAVY CHAIN V REGIONS)


Mass: 23761.291 Da / Num. of mol.: 1 / Fragment: FAB IMMUNOGLOBULIN FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C / References: UniProt: Q9R1A5, UniProt: P01837*PLUS
#2: Antibody PROTEIN (IG HEAVY CHAIN V REGIONS)


Mass: 23157.723 Da / Num. of mol.: 1 / Fragment: FAB IMMUNOGLOBULIN FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C / References: UniProt: P01867
#3: Antibody PROTEIN (IG HEAVY CHAIN V REGIONS)


Mass: 23678.049 Da / Num. of mol.: 1 / Fragment: FAB IMMUNOGLOBULIN FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C / References: UniProt: Q9R1A5, UniProt: I6L958*PLUS
#4: Antibody PROTEIN (IG HEAVY CHAIN V REGIONS)


Mass: 23398.234 Da / Num. of mol.: 1 / Fragment: FAB IMMUNOGLOBULIN FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C / References: UniProt: P01869
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.8 Å3/Da / Density % sol: 55.84 %
Crystal growpH: 4.9
Details: 12% PEG 800, 75 MILLIMOLAR SODIUM ACETATE PH 4.85 10MGM/ML PROTEIN CONCENTRATION , pH 4.9

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorDetector: AREA DETECTOR / Date: Nov 1, 1987
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→13.7 Å / Num. obs: 33526 / % possible obs: 97 % / Redundancy: 2.84 % / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassification
ROTAVATAdata reduction
Agrovatadata reduction
AMoREphasing
PROFFTrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FAB D1.3

Resolution: 2.5→7 Å / σ(F): 2.5 /
RfactorNum. reflection
Rwork0.179 -
obs-26929
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 7 Å
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 0 128 6733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.042
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.044
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.12
X-RAY DIFFRACTIONp_mcangle_it2.1
X-RAY DIFFRACTIONp_scbond_it1.6
X-RAY DIFFRACTIONp_scangle_it2.62
X-RAY DIFFRACTIONp_plane_restr0.01
X-RAY DIFFRACTIONp_chiral_restr0.115
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.1
X-RAY DIFFRACTIONp_staggered_tor22.3
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS

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