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- PDB-1f11: F124 FAB FRAGMENT FROM A MONOCLONAL ANTI-PRES2 ANTIBODY -

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Basic information

Entry
Database: PDB / ID: 1f11
TitleF124 FAB FRAGMENT FROM A MONOCLONAL ANTI-PRES2 ANTIBODY
Components
  • F124 IMMUNOGLOBULIN (IGG1 HEAVY CHAIN)
  • F124 IMMUNOGLOBULIN (KAPPA LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / immunoglobulin / antibody / fab / hepatitis B / preS2
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 / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / positive regulation of immune response / antibacterial humoral response / adaptive immune response / defense response to bacterium / immune response / external side of plasma membrane / extracellular space / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 kappa chain V-III region PC 7043 / Immunoglobulin kappa constant / Ig gamma-1 chain C region, membrane-bound form / Ab 126.33 heavy chain variable and joining regions / Ig-like domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSaul, F.A. / Vulliez-Le Normand, B. / Passafiume, M. / Riottot, M.M. / Bentley, G.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure of the Fab fragment from F124, a monoclonal antibody specific for hepatitis B surface antigen.
Authors: Saul, F.A. / Vulliez-Le Normand, B. / Passafiume, M. / Riottot, M.M. / Bentley, G.A.
#1: Journal: FEBS Lett. / Year: 1998
Title: Sequence Analysis of a Monoclonal Antibody Specific for the preS2 Region of Hepatitis B Surface Antigen, and the Cloning, Expression and Characterisation of its Single-chain Fv Construction
Authors: Passafiume, M. / Vulliez-le Normand, B. / Riottot, M.M. / Bentley, G.A.
History
DepositionMay 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_nat ...entity / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _struct_ref.db_code ..._entity.pdbx_fragment / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.4Aug 9, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _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: F124 IMMUNOGLOBULIN (KAPPA LIGHT CHAIN)
B: F124 IMMUNOGLOBULIN (IGG1 HEAVY CHAIN)
C: F124 IMMUNOGLOBULIN (KAPPA LIGHT CHAIN)
D: F124 IMMUNOGLOBULIN (IGG1 HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)95,1594
Polymers95,1594
Non-polymers00
Water0
1
A: F124 IMMUNOGLOBULIN (KAPPA LIGHT CHAIN)
B: F124 IMMUNOGLOBULIN (IGG1 HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,5802
Polymers47,5802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-20 kcal/mol
Surface area19250 Å2
MethodPISA
2
C: F124 IMMUNOGLOBULIN (KAPPA LIGHT CHAIN)
D: F124 IMMUNOGLOBULIN (IGG1 HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,5802
Polymers47,5802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-20 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.7, 54.0, 120.0
Angle α, β, γ (deg.)90.0, 101.0, 90.0
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody F124 IMMUNOGLOBULIN (KAPPA LIGHT CHAIN)


Mass: 23985.342 Da / Num. of mol.: 2
Fragment: FAB FRAGMENT (UNP P01665 residues 1-111, P01837 residues 1-106)
Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01665, UniProt: P01837
#2: Antibody F124 IMMUNOGLOBULIN (IGG1 HEAVY CHAIN)


Mass: 23594.383 Da / Num. of mol.: 2
Fragment: FAB FRAGMENT (UNP Q65ZR6 residues 18-134, P01869 residues 2-102)
Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q65ZR6, UniProt: P01869, UniProt: Q9D8L4*PLUS
Compound detailsantibody F124 (isotype IgG1, kappa light chain) recognizes an epitope in the segment 120-132 of the ...antibody F124 (isotype IgG1, kappa light chain) recognizes an epitope in the segment 120-132 of the preS2 region of the hepatitis B surface antigen.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 400, sodium acetate, ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate1reservoir
20.1 Msodium acetate1reservoir
35 %PEG4001reservoir
42.4 mg/mlprotein1drop
50.57 Mammonium sulfate1drop
60.028 Msodium acetate1drop
71.4 %PEG4001drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.96
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 17261 / Num. obs: 17261 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 6.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1665 / % possible all: 97.5
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 97.5 % / Num. unique obs: 1665

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IGI

1igi


Resolution: 3→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: A bulk solvent model was used. Non-crystallographic symmetry restraints were applied. NCS GROUP 1: chains A,C (1 to 109). NCS GROUP 2: chains A,C (114 to 198, 203 to 212). NCS GROUP 3: ...Details: A bulk solvent model was used. Non-crystallographic symmetry restraints were applied. NCS GROUP 1: chains A,C (1 to 109). NCS GROUP 2: chains A,C (114 to 198, 203 to 212). NCS GROUP 3: chains B,D (1 to 40, 43 to 112). NCS GROUP 4: chains B,D (115 to 127, 137 to 227).
RfactorNum. reflection% reflectionSelection details
Rfree0.271 878 5 %RANDOM
Rwork0.184 ---
all0.191 17261 --
obs0.191 17261 99.2 %-
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6598 0 0 0 6598
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d29.7
X-RAY DIFFRACTIONx_improper_angle_d0.68
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it2.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.35 124 5 %
Rwork0.25 1991 -
obs--98 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.68
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2.5
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.35 / % reflection Rfree: 5 % / Rfactor Rwork: 0.25 / Rfactor obs: 0.271

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