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- PDB-1bbj: CRYSTAL STRUCTURE OF A CHIMERIC FAB' FRAGMENT OF AN ANTIBODY BIND... -

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Basic information

Entry
Database: PDB / ID: 1bbj
TitleCRYSTAL STRUCTURE OF A CHIMERIC FAB' FRAGMENT OF AN ANTIBODY BINDING TUMOUR CELLS
Components
  • IGG4-KAPPA B72.3 FAB (HEAVY CHAIN)
  • IGG4-KAPPA B72.3 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis ...IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / 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 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin heavy constant gamma 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.1 Å
AuthorsBrady, R.L. / Hubbard, R.E. / Todd, R.J.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Crystal structure of a chimeric Fab' fragment of an antibody binding tumour cells.
Authors: Brady, R.L. / Edwards, D.J. / Hubbard, R.E. / Jiang, J.S. / Lange, G. / Roberts, S.M. / Todd, R.J. / Adair, J.R. / Emtage, J.S. / King, D.J. / Low, D.C.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Preliminary X-Ray Diffraction Study of a Chimeric Fab' Fragment of an Antibody Binding Tumour Cells
Authors: Brady, R.L. / Hubbard, R.E. / King, D.J. / Low, D.C. / Roberts, S.M. / Todd, R.J.
History
DepositionApr 30, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2014Group: Source and taxonomy
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG4-KAPPA B72.3 FAB (LIGHT CHAIN)
H: IGG4-KAPPA B72.3 FAB (HEAVY CHAIN)
A: IGG4-KAPPA B72.3 FAB (LIGHT CHAIN)
B: IGG4-KAPPA B72.3 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)91,8864
Polymers91,8864
Non-polymers00
Water00
1
L: IGG4-KAPPA B72.3 FAB (LIGHT CHAIN)
H: IGG4-KAPPA B72.3 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)45,9432
Polymers45,9432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-26 kcal/mol
Surface area18760 Å2
MethodPISA
2
A: IGG4-KAPPA B72.3 FAB (LIGHT CHAIN)
B: IGG4-KAPPA B72.3 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)45,9432
Polymers45,9432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-25 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.500, 93.200, 208.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO L 8
2: ASN L 28 - ILE L 29 OMEGA =145.72 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO L 95 / 4: CIS PROLINE - PRO L 141 / 5: CIS PROLINE - PRO H 148 / 6: CIS PROLINE - PRO H 150
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999867, -0.01191, 0.011172), (0.011579, 0.999506, 0.029227), (-0.011515, -0.029094, 0.99951)
Vector: -0.2079, -47.9869, -23.807)
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO FAB MOLECULES. ONLY ONE MOLECULE IS PRESENTED IN THIS ENTRY. THE OTHER MOLECULE MAY BE GENERATED USING THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW.

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Components

#1: Antibody IGG4-KAPPA B72.3 FAB (LIGHT CHAIN)


Mass: 23152.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Cricetulus griseus (Chinese hamster) / References: GenBank: 11692743
#2: Antibody IGG4-KAPPA B72.3 FAB (HEAVY CHAIN)


Mass: 22790.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01861
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.57 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlFab'11
250 mMsodium phosphate11
32.21 Mammonium sulphate12
45 %(v/v)dioxan12
550 mMsodium phosphate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.1 Å / Num. obs: 15644 / % possible obs: 74 % / Num. measured all: 57781 / Rmerge(I) obs: 0.068

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.176 / Highest resolution: 3.1 Å
Refinement stepCycle: LAST / Highest resolution: 3.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 0 0 6466
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d3.73
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 15 Å / Rfactor obs: 0.176 / Num. reflection obs: 15644
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.87 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d3.73
X-RAY DIFFRACTIONp_angle_deg3.73
LS refinement shell
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3.34 Å / Total num. of bins used: 5 / Rfactor obs: 0.2424

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