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- PDB-1yek: CATALYTIC ANTIBODY D2.3 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1yek
TitleCATALYTIC ANTIBODY D2.3 COMPLEX
Components
  • PROTEIN (IG ANTIBODY D2.3 (HEAVY CHAIN))
  • PROTEIN (IG ANTIBODY D2.3 (LIGHT CHAIN))
KeywordsIMMUNE SYSTEM / ABZYME / REACTION PRODUCT
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / immune response / extracellular space / metal ion binding
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 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
P-NITROPHENOL / Ig gamma-2A chain C region, A allele / Igk protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGigant, B. / Knossow, M.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Crossreactivity, efficiency and catalytic specificity of an esterase-like antibody.
Authors: Gigant, B. / Charbonnier, J.B. / Eshhar, Z. / Green, B.S. / Knossow, M.
History
DepositionAug 13, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PROTEIN (IG ANTIBODY D2.3 (LIGHT CHAIN))
H: PROTEIN (IG ANTIBODY D2.3 (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,80610
Polymers48,2092
Non-polymers5978
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-193 kcal/mol
Surface area19460 Å2
MethodPISA
2
L: PROTEIN (IG ANTIBODY D2.3 (LIGHT CHAIN))
hetero molecules

H: PROTEIN (IG ANTIBODY D2.3 (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,80610
Polymers48,2092
Non-polymers5978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_665x-y+1,-y+1,-z+2/31
Buried area1710 Å2
ΔGint-210 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.730, 78.730, 159.030
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 PROTEIN (IG ANTIBODY D2.3 (LIGHT CHAIN))


Mass: 24019.842 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q58EU8*PLUS
#2: Antibody PROTEIN (IG ANTIBODY D2.3 (HEAVY CHAIN))


Mass: 24189.217 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01863*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS. (RESIDUES H106 - H223) AND OF THE LIGHT ...THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS. (RESIDUES H106 - H223) AND OF THE LIGHT CHAINS (RESIDUES L107 - L214) 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. NPO IS PARA-NITROPHENOL

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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: 2.95 Å3/Da / Density % sol: 57 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH 6.0, 40MM ZN ACETATE, VAPOR DIFFUSION, HANGING DROP
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
230 %(v/v)PEG6001reservoir
340 mMzinc acetate1reservoir
4100 mMcacodylate1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 19, 1996 / Details: BENT MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→17 Å / Num. obs: 33481 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rsym value: 0.071 / Net I/σ(I): 9.5
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.401 / % possible all: 97.7
Reflection
*PLUS
Num. measured all: 84756 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 97.7 % / Rmerge(I) obs: 0.401

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Processing

Software
NameVersionClassification
MOSFLM5.2data reduction
Agrovatadata reduction
AMoREphasing
X-PLOR3.843refinement
Agrovatadata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YEC

1yec


Resolution: 2.1→7 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1619 5 %RANDOM
Rwork0.2 ---
obs0.2 31743 98.7 %-
Displacement parametersBiso mean: 30 Å2
Refine analyzeLuzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 17 142 3548
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_deg1.671
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.54
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.379
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: 2.1→2.19 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.297 198 5 %
Rwork0.291 3637 -
obs--95.8 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 7 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.54
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.379
LS refinement shell
*PLUS
Rfactor Rfree: 0.297 / % reflection Rfree: 5 % / Rfactor Rwork: 0.291 / Rfactor obs: 0.291

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