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- PDB-1flr: 4-4-20 FAB FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1flr
Title4-4-20 FAB FRAGMENT
Components(4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT) x 2
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: 1.85 Å
AuthorsWhitlow, M.
Citation
Journal: Protein Eng. / Year: 1995
Title: 1.85 A structure of anti-fluorescein 4-4-20 Fab.
Authors: Whitlow, M. / Howard, A.J. / Wood, J.F. / Voss Jr., E.W. / Hardman, K.D.
#1: 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. / Mason, M.L. / Voss Junior, E.W. / Edmundson, A.B.
#2: 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. / Voss Junior, E.W. / Edmundson, A.B.
#3: Journal: J.Biol.Chem. / Year: 1989
Title: Comparison of Variable Region Primary Structures within an Anti-Fluorescein Idiotype Family
Authors: Bedzyk, W.D. / Johnson, L.S. / Riordon, G.S. / Voss, E.W.
History
DepositionJan 19, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT
H: 4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4803
Polymers48,1482
Non-polymers3321
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-27 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.750, 43.870, 58.170
Angle α, β, γ (deg.)95.15, 86.85, 98.01
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 100 / 3: CIS PROLINE - PRO L 146 / 4: CIS PROLINE - PRO H 152 / 5: CIS PROLINE - PRO H 194 / 6: WATER MOLECULE 870 IS DISORDERED.

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Components

#1: Antibody 4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT


Mass: 24173.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: LYMPHOCYTE-PLASMA CELL / Cell line: 4-4-20 MURINE-MURINE HYBRIDOMA / Organ: SPLEEN / Variant: BALB/CV / Strain: BALB/C / References: GenBank: 1589925
#2: Antibody 4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT


Mass: 23973.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: LYMPHOCYTE-PLASMA CELL / Cell line: 4-4-20 MURINE-MURINE HYBRIDOMA / Organ: SPLEEN / Variant: BALB/CV / Strain: BALB/C / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: unknown
Details: Gibson, A.L., (1988) Proteins: Struct.,Funct., Genet., 3, 155.
PH range low: 7.3 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMsodium phosphate11
214-30 mg/mlprotein11
325-50 %(w/v)PEG335012

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Oct 21, 1988
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 29963 / % possible obs: 70 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.041
Reflection
*PLUS
Highest resolution: 1.79 Å / Num. measured all: 76616 / Rmerge(I) obs: 0.041

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Processing

Software
NameClassification
XENGENdata collection
PROFFTrefinement
XENGENdata reduction
RefinementResolution: 1.85→10 Å / σ(F): 2
Details: RESIDUES CYS H 133 TO GLY H 138 ARE IN WEAK ELECTRON DENSITY. THERE IS A DISCONTINUITY IN THE ELECTION DENSITY MAP BETWEEN RESIDUES VAL H 132 AND CYS H 133. THE RESULTING COORDINATES, AS ...Details: RESIDUES CYS H 133 TO GLY H 138 ARE IN WEAK ELECTRON DENSITY. THERE IS A DISCONTINUITY IN THE ELECTION DENSITY MAP BETWEEN RESIDUES VAL H 132 AND CYS H 133. THE RESULTING COORDINATES, AS PRESENTED IN THIS ENTRY, CONTAIN TWO POSITIONS FOR N CYS H 133, ONE OF WHICH IS PROPERLY CONNECTED TO C VAL H 132 BUT QUITE DISTANT (5.58 ANGSTROMS) FROM CA CYS H 133. THE OTHER POSITION FOR N CYS H 133 IS PROPERLY CONNECTED TO CA H 133 BUT QUITE DISTANT (4.51 ANGSTROMS) FROM C VAL H 132.
RfactorNum. reflection
obs0.188 26328
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 25 290 3665
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.015
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it16.8711
X-RAY DIFFRACTIONp_mcangle_it17.1071.5
X-RAY DIFFRACTIONp_scbond_it19.1441.5
X-RAY DIFFRACTIONp_scangle_it20.5062
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1910.15
X-RAY DIFFRACTIONp_singtor_nbd0.1910.5
X-RAY DIFFRACTIONp_multtor_nbd0.2710.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3050.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor21.415
X-RAY DIFFRACTIONp_orthonormal_tor26.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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