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- PDB-1igt: STRUCTURE OF IMMUNOGLOBULIN -

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Basic information

Entry
Database: PDB / ID: 1igt
TitleSTRUCTURE OF IMMUNOGLOBULIN
Components(IGG2A INTACT ANTIBODY - MAB231) x 2
KeywordsIMMUNOGLOBULIN / INTACT IMMUNOGLOBULIN V REGION C REGION
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / extracellular space / plasma membrane
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
Ig gamma-2A chain C region, A allele
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHarris, L.J. / Larson, S.B. / Hasel, K.W. / McPherson, A.
Citation
Journal: Biochemistry / Year: 1997
Title: Refined structure of an intact IgG2a monoclonal antibody.
Authors: Harris, L.J. / Larson, S.B. / Hasel, K.W. / McPherson, A.
#1: Journal: Nature / Year: 1992
Title: The Three-Dimensional Structure of an Intact Monoclonal Antibody for Canine Lymphoma
Authors: Harris, L.J. / Larson, S.B. / Hasel, K.W. / Day, J. / Greenwood, A. / McPherson, A.
History
DepositionOct 25, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: 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 / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_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_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
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_atoms
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: IGG2A INTACT ANTIBODY - MAB231
B: IGG2A INTACT ANTIBODY - MAB231
C: IGG2A INTACT ANTIBODY - MAB231
D: IGG2A INTACT ANTIBODY - MAB231
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,6826
Polymers145,4314
Non-polymers3,2512
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16590 Å2
ΔGint-21 kcal/mol
Surface area64330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.820, 76.770, 100.640
Angle α, β, γ (deg.)88.05, 92.35, 97.23
Int Tables number1
Space group name H-MP1
DetailsTHERE IS ONE ENTIRE ANTIBODY MOLECULE PER ASYMMETRIC UNIT.

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Components

#1: Antibody IGG2A INTACT ANTIBODY - MAB231


Mass: 23420.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: HYBRIDOMA MONOCLONAL ANTIBODY / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#2: Antibody IGG2A INTACT ANTIBODY - MAB231


Mass: 49294.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: HYBRIDOMA MONOCLONAL ANTIBODY / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: UniProt: P01863
#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-beta-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]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-3-1-3-1-4-5/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-beta-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]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4-5/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: 13

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63 %
Description: THE MULTIWIRE AND SYNCHROTRON DATA SETS WERE CUT AT F > 4SIGMA, AND THEN MERGED TO YIELD THE FINAL REDUCED DATA SET OF 41371 UNIQUE REFLECTIONS AT 2.8-20 A; RMERGE = 6.7%. THIS COMBINED ...Description: THE MULTIWIRE AND SYNCHROTRON DATA SETS WERE CUT AT F > 4SIGMA, AND THEN MERGED TO YIELD THE FINAL REDUCED DATA SET OF 41371 UNIQUE REFLECTIONS AT 2.8-20 A; RMERGE = 6.7%. THIS COMBINED DATA WAS USED FOR REFINEMENT.
Crystal growTemperature: 291 K / pH: 8
Details: 7 MICROLITERS OF 4.3 MG/ML MAB231, 3 MICROLITERS 50 MILLIMOLAR TRIS PH 8.0, AND 7 MICROLITERS 4% PEG 3350 EQUILIBRATED AGAINST 25 ML RESERVOIRS OF 4% PEG 3350, AT 18 DEGREE CELSIUS (SANDWICH ...Details: 7 MICROLITERS OF 4.3 MG/ML MAB231, 3 MICROLITERS 50 MILLIMOLAR TRIS PH 8.0, AND 7 MICROLITERS 4% PEG 3350 EQUILIBRATED AGAINST 25 ML RESERVOIRS OF 4% PEG 3350, AT 18 DEGREE CELSIUS (SANDWICH PLATE)., temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion / Details: Larson, S., (1991) J. Mol. Biol., 222, 17. / PH range low: 8.2 / PH range high: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.1 mg/mlprotein1drop
20.01 MTris-HCl1drop
31.8 %PEG33501drop
44 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 1, 1992
RadiationMonochromator: SUPPER GRAPHITE CRYSTAL ASYMMETRIC CUT TRIANGULAR BENT CRYSTAL (SI-111)
Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→76.1 Å / Num. obs: 47595 / % possible obs: 99 % / Redundancy: 4.4 % / Biso Wilson estimate: 45.5 Å2 / Rsym value: 0.1 / Net I/σ(I): 7.1
Reflection
*PLUS
Num. measured all: 200000 / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
HOWARDdata collection
NIELSENdata collection
HOWARDdata reduction
NIELSENdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGEN(HOWARDdata reduction
XUONG)data reduction
XENGEN(HOWARDdata scaling
NIELSENdata scaling
XUONG)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VL:VH DOMAIN PAIR OF PDB ENTRY 1MCP, CL:CH1 DOMAIN PAIR OF ENTRY 2HFL, FC FRAGMENT OF ENTRY 1FC1

1mcp

2hfl
PDB Unreleased entry

1fc1


Resolution: 2.8→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4
Details: BULK SOLVENT MODEL USED GROUP 1 POSITIONAL (CL) (A) : 0.05 ; 200 GROUP 2 POSITIONAL (CH1) (A) : 0.05 ; 200 GROUP 3 POSITIONAL (CH2) (A) : 0.06 ; 200 GROUP 4 POSITIONAL (CH3) (A) : 0.05 ; 200 ...Details: BULK SOLVENT MODEL USED GROUP 1 POSITIONAL (CL) (A) : 0.05 ; 200 GROUP 2 POSITIONAL (CH1) (A) : 0.05 ; 200 GROUP 3 POSITIONAL (CH2) (A) : 0.06 ; 200 GROUP 4 POSITIONAL (CH3) (A) : 0.05 ; 200 BACKBONE ATOMS ONLY WERE RESTRAINED BY NCS AND RESIDUES INVOLVED IN PACKING WERE NOT RESTRAINED. NCS B-FACTOR RESTRAINTS WERE NOT EMPLOYED.
RfactorNum. reflection% reflectionSelection details
Rfree0.297 4149 10 %RANDOM
Rwork0.209 ---
obs0.209 41371 86.2 %-
Displacement parametersBiso mean: 52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10214 0 220 0 10434
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it5.91.5
X-RAY DIFFRACTIONx_mcangle_it9.62
X-RAY DIFFRACTIONx_scbond_it7.882
X-RAY DIFFRACTIONx_scangle_it11.392.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 487 9.8 %
Rwork0.322 4482 -
obs--62 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3_MOD2.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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