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- PDB-1yed: STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.4) -

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Basic information

Entry
Database: PDB / ID: 1yed
TitleSTRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.4)
Components(IGG1 FAB FRAGMENT (D.2.4)) x 2
KeywordsCATALYTIC ANTIBODY / TRANSITION STATE ANALOGUE
Function / homology
Function and homology information


phagocytosis, recognition / 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 / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding ...phagocytosis, recognition / 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 / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / cytoplasm
Similarity search - Function
: / 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 ...: / 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
4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE / : / Ig gamma-1 chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGolinelli-Pimpaneau, B. / Knossow, M.
CitationJournal: Science / Year: 1997
Title: Structural convergence in the active sites of a family of catalytic antibodies.
Authors: Charbonnier, J.B. / Golinelli-Pimpaneau, B. / Gigant, B. / Tawfik, D.S. / Chap, R. / Schindler, D.G. / Kim, S.H. / Green, B.S. / Eshhar, Z. / Knossow, M.
History
DepositionApr 15, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: IGG1 FAB FRAGMENT (D.2.4)
A: IGG1 FAB FRAGMENT (D.2.4)
H: IGG1 FAB FRAGMENT (D.2.4)
B: IGG1 FAB FRAGMENT (D.2.4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9066
Polymers97,1854
Non-polymers7212
Water724
1
L: IGG1 FAB FRAGMENT (D.2.4)
H: IGG1 FAB FRAGMENT (D.2.4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9533
Polymers48,5932
Non-polymers3601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-19 kcal/mol
Surface area20070 Å2
MethodPISA
2
A: IGG1 FAB FRAGMENT (D.2.4)
B: IGG1 FAB FRAGMENT (D.2.4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9533
Polymers48,5932
Non-polymers3601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-19 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.250, 104.790, 223.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.054319, -0.998513, -0.004603), (-0.998512, 0.05434, -0.004596), (0.004839, 0.004347, -0.999979)
Vector: 51.75388, 98.82323, 55.75489)

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Components

#1: Antibody IGG1 FAB FRAGMENT (D.2.4)


Mass: 24092.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TRANSITION STATE ANALOGUE / Source: (natural) Mus musculus (house mouse) / References: PIR: S16112
#2: Antibody IGG1 FAB FRAGMENT (D.2.4)


Mass: 24499.615 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TRANSITION STATE ANALOGUE / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01868
#3: Chemical ChemComp-PNB / 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE


Mass: 360.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 12, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.375 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 18722 / % possible obs: 87.6 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
MOSFLM5.2data reduction
CCP4data reduction
X-PLOR3.84model building
X-PLOR3.84refinement
CCP4data scaling
X-PLOR3.84phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YEC FOR THE VARIABLE DOMAINS AND PDB ENTRY 1DFB FOR THE CONSTANT DOMAINS

1yec

1dfb


Resolution: 3.1→7 Å / σ(F): 2
Details: RESIDUES POORLY DEFINED BY THE ELECTRON DENSITY: CHAINS L, A: 1, 157 - 160, 198 - 207, 220 - 222 CHAINS H, B: 129 - 137, 173 - 175, 187 - 193, 214 - 217
RfactorNum. reflection% reflection
Rfree0.26 -5 %
Rwork0.215 --
obs0.215 50937 -
Refinement stepCycle: LAST / Resolution: 3.1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6834 0 48 4 6886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.647
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.02
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.408
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.02
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.408

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