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Basic information

Entry
Database: PDB / ID: 1igy
TitleSTRUCTURE OF IMMUNOGLOBULIN
Components(IGG1 INTACT ANTIBODY MAB61.1.3) x 2
KeywordsIMMUNOGLOBULIN / INTACT IMMUNOGLOBULIN / V REGION / C REGION / HINGE REGION
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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
: / : / Immunoglobulin kappa constant / Ig gamma-1 chain C region, membrane-bound form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHarris, L.J. / McPherson, A.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystallographic structure of an intact IgG1 monoclonal antibody.
Authors: Harris, L.J. / Skaletsky, E. / McPherson, A.
#1: Journal: Proteins / Year: 1995
Title: Crystallization of Intact Monoclonal Antibodies
Authors: Harris, L.J. / Skaletsky, E. / McPherson, A.
History
DepositionOct 9, 1997Processing site: BNL
Revision 1.0Apr 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGG1 INTACT ANTIBODY MAB61.1.3
B: IGG1 INTACT ANTIBODY MAB61.1.3
C: IGG1 INTACT ANTIBODY MAB61.1.3
D: IGG1 INTACT ANTIBODY MAB61.1.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,1056
Polymers142,8544
Non-polymers3,2512
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16030 Å2
ΔGint-2 kcal/mol
Surface area61430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.650, 190.660, 73.100
Angle α, β, γ (deg.)90.00, 109.66, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHERE IS ONE ENTIRE ANTIBODY MOLECULE PER ASYMMETRIC UNIT.

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Components

#1: Antibody IGG1 INTACT ANTIBODY MAB61.1.3


Mass: 23519.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: HYBRIDOMA MONOCLONAL ANTIBODY, AGAINST PHENOBARBITAL
Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: GenBank: 309359, UniProt: P01837*PLUS
#2: Antibody IGG1 INTACT ANTIBODY MAB61.1.3


Mass: 47906.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: HYBRIDOMA MONOCLONAL ANTIBODY, AGAINST PHENOBARBITAL
Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: GenBank: 194362, UniProt: P01869*PLUS
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAca1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/6,9,8/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-2-3-4-1-4-1-5-6/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAca1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/6,9,8/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3-4-1-4-1-5-6/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
Sequence detailsTHE INTACT ANTIBODY IS NUMBERED ACCORDING TO THE CONVENTION OF E. KABAT [KABAT ET AL. (1991) ...THE INTACT ANTIBODY IS NUMBERED ACCORDING TO THE CONVENTION OF E. KABAT [KABAT ET AL. (1991) SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 5TH ED., NATIONAL INSTITUTES OF HEALTH, BETHESDA, MD].

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growpH: 5.1
Details: 4 MICROLITERS OF 8.7 MG/ML MAB 61.1.3, 2 MICROLITERS OF 50 MILLIMOLAR SODIUM CITRATE PH 5, 1 MICROLITER OF N-TRIDECYL-B-D-MALTOSIDE, AND 5 MICROLITERS OF 12% PEG 3350 EQUILIBRATED AGAINST ...Details: 4 MICROLITERS OF 8.7 MG/ML MAB 61.1.3, 2 MICROLITERS OF 50 MILLIMOLAR SODIUM CITRATE PH 5, 1 MICROLITER OF N-TRIDECYL-B-D-MALTOSIDE, AND 5 MICROLITERS OF 12% PEG 3350 EQUILIBRATED AGAINST 700 MICROLITERS OF 12% PEG 3350, AT ROOM TEMPERATURE (CRYSCHEM PLATE)., pH 5.1
Temp details: room temp
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Details: Harris, L.J., (1995) Proteins: Struct.,Funct., Genet., 23, 285.
PH range low: 5 / PH range high: 4.5
Components of the solutions
*PLUS
Conc.: 12 %(w/v) / Common name: PEG3350

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: MIRROR
RadiationMonochromator: CRYSTAL TYPE SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 3.2→99 Å / Num. obs: 27971 / % possible obs: 95.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 6.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VL:VH DOMAIN PAIR OF PDB ENTRY 1MCP, CL:CH1 DOMAIN PAIR OF PDB ENTRY 2HFL, FC FRAGMENT OF PDB ENTRY 1IGT

1mcp

2hfl
PDB Unreleased entry

1igt


Resolution: 3.2→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 3
Details: BULK SOLVENT MODEL USED. THE LOWER HINGE REGION OF CHAIN B WAS DISORDERED BUT MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.327 2064 9.8 %RANDOM
Rwork0.211 ---
obs0.211 21145 75 %-
Displacement parametersBiso mean: 57.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.88 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10032 0 220 0 10252
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.35
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
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 175 8.8 %
Rwork0.284 1815 -
obs--42.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3_MOD2.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 19081
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.35

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