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- PDB-1bm3: IMMUNOGLOBULIN OPG2 FAB-PEPTIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1bm3
TitleIMMUNOGLOBULIN OPG2 FAB-PEPTIDE COMPLEX
Components
  • IMMUNOGLOBULIN OPG2 FAB, CONSTANT DOMAIN
  • IMMUNOGLOBULIN OPG2 FAB, VARIABLE DOMAIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN
Function / homology
Function and homology information


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 / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding ...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 / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / plasma membrane / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig gamma-1 chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKodandapani, R. / Veerapandian, L. / Ni, C.Z. / Chiou, C.-K. / Whital, R. / Kunicki, T.J. / Ely, K.R.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 1998
Title: Conformational change in an anti-integrin antibody: structure of OPG2 Fab bound to a beta 3 peptide.
Authors: Kodandapani, R. / Veerapandian, L. / Ni, C.Z. / Chiou, C.K. / Whittal, R.M. / Kunicki, T.J. / Ely, K.R.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Crystal structure of the OPG2 Fab. An antireceptor antibody that mimics an RGD cell adhesion site.
Authors: Kodandapani, R. / Veerapandian, B. / Kunicki, T.J. / Ely, K.R.
History
DepositionApr 15, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 20, 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
Revision 1.4Nov 27, 2019Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IMMUNOGLOBULIN OPG2 FAB, CONSTANT DOMAIN
H: IMMUNOGLOBULIN OPG2 FAB, VARIABLE DOMAIN


Theoretical massNumber of molelcules
Total (without water)48,0582
Polymers48,0582
Non-polymers00
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-27 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.110, 90.050, 79.110
Angle α, β, γ (deg.)90.00, 115.30, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MA121

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Components

#1: Antibody IMMUNOGLOBULIN OPG2 FAB, CONSTANT DOMAIN


Mass: 23549.811 Da / Num. of mol.: 1 / Fragment: CONSTANT DOMAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody IMMUNOGLOBULIN OPG2 FAB, VARIABLE DOMAIN


Mass: 24508.473 Da / Num. of mol.: 1 / Fragment: VARIABLE DOMAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01868*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.44 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.5
Details: 0.1M CACODYLATE, PH6.5, 0.2M CALCIUM ACETATE AND 16% PEG 8000
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
121 mg/mlprotein/peptide1drop
216 %PEG80001reservoir
30.1 Mcacodylate1reservoir
40.2 Mcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Mar 12, 1992
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 20334 / % possible obs: 78 % / Observed criterion σ(I): 3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.044 / Rsym value: 0.054

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Processing

Software
NameVersionClassification
UCSD-systemAREA DETECTOR PROGRAMSdata collection
NILSENdata reduction
X-PLOR3.851refinement
UCSD-systemdata reduction
X-GEN(HOWARDdata scaling
NILSENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OPG

1opg


Resolution: 2→8 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.152 --
obs-20334 78 %
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 0 313 3589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg0.062
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 / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_deg0.045
X-RAY DIFFRACTIONx_planar_d0.0350.041
X-RAY DIFFRACTIONx_plane_restr0.020.015

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