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- PDB-1yef: STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH SUBSTRATE A... -

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Basic information

Entry
Database: PDB / ID: 1yef
TitleSTRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH SUBSTRATE ANALOGUE
Components(IGG2A FAB FRAGMENT) x 2
KeywordsCATALYTIC ANTIBODY
Function / homology
Function and homology information


immunoglobulin receptor binding
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
PARA-NITROBENZYL GLUTARYL GLYCINIC ACID / : / Ig gamma-2A chain C region, A allele
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGigant, B. / Knossow, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: X-ray structures of a hydrolytic antibody and of complexes elucidate catalytic pathway from substrate binding and transition state stabilization through water attack and product release.
Authors: Gigant, B. / Charbonnier, J.B. / Eshhar, Z. / Green, B.S. / Knossow, M.
History
DepositionMay 29, 1997Processing site: BNL
Revision 1.0Dec 3, 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 / software / 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 / _software.name / _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 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: IGG2A FAB FRAGMENT
H: IGG2A FAB FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,04211
Polymers48,1952
Non-polymers8479
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.200, 78.200, 158.700
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


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


Mass: 24189.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01863
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PNC / PARA-NITROBENZYL GLUTARYL GLYCINIC ACID


Mass: 323.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N3O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS (RESIDUES H 106 - H 223) AND OF THE LIGHT ...THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS (RESIDUES H 106 - H 223) AND OF THE LIGHT CHAINS (RESIDUES L 107 - L 214) HAVE NOT BEEN DETERMINED FOR THIS IMMUNOGLOBULIN. THEY HAVE BEEN ASSIGNED THE CONSENSUS SEQUENCE FOR THE CONSTANT DOMAIN OF MOUSE KAPPA LIGHT CHAIN AND FOR THE FIRST CONSTANT DOMAIN OF MOUSE GROUP 2A HEAVY CHAINS.

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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: 51.8 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP METHOD. PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
2100 mMcacodylate1drop
340 mMzinc acetate1reservoir
435 %(w/v)PEG6001reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.94
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 22, 1996 / Details: BENT MIRROR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 38114 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rsym value: 0.055 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.301 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 89942 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.301

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Processing

Software
NameVersionClassification
MOSFLM5.2data reduction
Agrovatadata reduction
X-PLOR3.84model building
X-PLOR3.84refinement
Agrovatadata scaling
X-PLOR3.84phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YEC

1yec


Resolution: 2→7 Å / σ(F): 2
Details: RESIDUES 212 - 214 OF THE LIGHT CHAIN AND 127 - 134 OF THE HEAVY CHAIN ARE POORLY DEFINED BY THE ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.248 1865 5 %
Rwork0.199 --
obs0.199 36515 98.8 %
Displacement parametersBiso mean: 29 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 31 160 3575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.715
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.62
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.431
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
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.308 222 5 %
Rwork0.288 4203 -
obs--98.7 %
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_deg28.626
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.431

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