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- PDB-4fab: THREE-DIMENSIONAL STRUCTURE OF A FLUORESCEIN-FAB COMPLEX CRYSTALL... -

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Basic information

Entry
Database: PDB / ID: 4fab
TitleTHREE-DIMENSIONAL STRUCTURE OF A FLUORESCEIN-FAB COMPLEX CRYSTALLIZED IN 2-METHYL-2,4-PENTANEDIOL
Components
  • IGG2A-KAPPA 4-4-20 FAB (HEAVY CHAIN)
  • IGG2A-KAPPA 4-4-20 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport ...positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport / antigen processing and presentation / immunoglobulin mediated immune response / regulation of proteolysis / positive regulation of endocytosis / complement activation, classical pathway / antigen binding / multivesicular body / positive regulation of phagocytosis / response to bacterium / positive regulation of immune response / 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
2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / : / Immunoglobulin heavy constant gamma 2A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsHerron, J.N. / He, X. / Mason, M.L. / Vossjunior, E.W. / Edmundson, A.B.
Citation
Journal: Proteins / Year: 1989
Title: Three-dimensional structure of a fluorescein-Fab complex crystallized in 2-methyl-2,4-pentanediol.
Authors: Herron, J.N. / He, X.M. / Mason, M.L. / Voss Jr., E.W. / Edmundson, A.B.
#1: Journal: Proteins / Year: 1988
Title: Differences in Crystal Properties and Ligand Affinities of an Antifluorescyl Fab (4-4-20) in Two Solvent Systems
Authors: Gibson, A.L. / Herron, J.N. / He, X.-M. / Patrick, V.A. / Mason, M.L. / Lin, J.-N. / Kranz, D.M. / Vossjunior, E.W. / Edmundson, A.B.
History
DepositionApr 10, 1989Processing site: BNL
Revision 1.0Jul 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Sep 27, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Non-polymer description / Other / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_database_status / pdbx_validate_close_contact
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_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2
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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG2A-KAPPA 4-4-20 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA 4-4-20 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3014
Polymers47,8502
Non-polymers4502
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-40 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.300, 43.900, 42.500
Angle α, β, γ (deg.)82.10, 87.30, 84.60
Int Tables number1
Space group name H-MP1
Atom site foot note1: RESIDUES PRO L 8, PRO L 100, PRO L 146, AND PRO H 152 ARE CIS PROLINES.

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Components

#1: Antibody IGG2A-KAPPA 4-4-20 FAB (LIGHT CHAIN)


Mass: 24187.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 1589925
#2: Antibody IGG2A-KAPPA 4-4-20 FAB (HEAVY CHAIN)


Mass: 23662.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01865
#3: Chemical ChemComp-FLU / 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / FLUORESCEIN


Mass: 332.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H12O5
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal grow
*PLUS
Temperature: 12-14 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
247 %MPD11
1protein110.040ml

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Data collection

Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 11116

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.7→6 Å / σ(I): 1.5 /
RfactorNum. reflection
obs0.215 8304
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 25 8 3395
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0280.03
X-RAY DIFFRACTIONp_angle_d0.0550.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.03
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_restr0.0140.025
X-RAY DIFFRACTIONp_chiral_restr0.210.15
X-RAY DIFFRACTIONp_singtor_nbd0.280.5
X-RAY DIFFRACTIONp_multtor_nbd0.40.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.4090.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.33
X-RAY DIFFRACTIONp_staggered_tor26.915
X-RAY DIFFRACTIONp_orthonormal_tor28.115
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS

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