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- PDB-1yec: STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.3) -

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Basic information

Entry
Database: PDB / ID: 1yec
TitleSTRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.3)
Components(IGG2A FAB FRAGMENT (D2.3)) x 2
KeywordsCATALYTIC ANTIBODY / TRANSITION STATE ANALOGUE
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response
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 / Immunoglobulins ...: / 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
4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE / : / Ig gamma-2A chain C region, A allele
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPACEMENT / Resolution: 1.9 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 3, 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 / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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 30, 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: IGG2A FAB FRAGMENT (D2.3)
H: IGG2A FAB FRAGMENT (D2.3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,01310
Polymers48,1952
Non-polymers8188
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-144 kcal/mol
Surface area19190 Å2
MethodPISA
2
L: IGG2A FAB FRAGMENT (D2.3)
hetero molecules

H: IGG2A FAB FRAGMENT (D2.3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,01310
Polymers48,1952
Non-polymers8188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_665x-y+1,-y+1,-z+2/31
Buried area1800 Å2
ΔGint-159 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.180, 78.180, 158.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody IGG2A FAB FRAGMENT (D2.3)


Mass: 24005.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CATALYTIC ANTIBODY, TRANSITION STATE ANALOGUE / Source: (natural) Mus musculus (house mouse) / References: PIR: S16112
#2: Antibody IGG2A FAB FRAGMENT (D2.3)


Mass: 24189.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CATALYTIC ANTIBODY, TRANSITION STATE ANALOGUE / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01863
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PNB / 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE


Mass: 360.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N2O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.901
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 27, 1995 / Details: BENT MIRROR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 44679 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Rmerge(I) obs: 0.063

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Processing

Software
NameVersionClassification
MOSFLM5.2data reduction
CCP4data reduction
AMoREphasing
X-PLOR3.84refinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPACEMENT
Starting model: PDB ENTRY 1KNO

1kno


Resolution: 1.9→7 Å / σ(F): 2
Details: RESIDUES POORLY DEFINED BY THE ELECTRON DENSITY: CHAIN L: 212 - 214 CHAIN H: 127 - 134
RfactorNum. reflection% reflection
Rfree0.252 -5 %
Rwork0.208 --
obs0.208 92749 98 %
Displacement parametersBiso mean: 35 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 31 150 3565
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.703
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.48
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.382
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_deg28.48
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.382

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