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- PDB-1yej: CATALYTIC ANTIBODY COMPLEX -

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Basic information

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


immunoglobulin complex / adaptive immune response / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
Chem-PNF / Igk protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 / 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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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)49,06910
Polymers48,2092
Non-polymers8608
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-172 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.271, 78.271, 158.674
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) / Cell: B-LYMPHOCYTE / Strain: BALB/C / 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) / Cell: B-LYMPHOCYTE / Strain: BALB/C
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PNF / 6-{4-[HYDROXY-(4-NITRO-PHENOXY)-PHOSPHORYL]-BUTYRYLAMINO}-HEXANOIC ACID


Mass: 402.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H23N2O8P
#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 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. PNF IS PARA-NITROPHENYL PHOSPHONATE GLUTARYL CAPROATE (NO2-C6H5-O-PO2-(CH2)3-CO-NH-(CH2)5-COOH)

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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 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE, VAPOR DIFFUSION, HANGING DROP
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃
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: Jul 12, 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: 1.85→10 Å / Num. obs: 46997 / % possible obs: 96.9 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Rsym value: 0.065 / Net I/σ(I): 17.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.65 / Rsym value: 0.404 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 105615 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 98.8 % / Rmerge(I) obs: 0.404

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Processing

Software
NameVersionClassification
DENZO1.6data reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YEC

1yec


Resolution: 1.85→7 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2313 5 %RANDOM
Rwork0.212 ---
obs0.212 45666 96.9 %-
Displacement parametersBiso mean: 28 Å2
Refine analyzeLuzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.85→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 34 163 3586
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_deg2.324
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.42
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.362
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: 1.85→1.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.313 282 5 %
Rwork0.304 5354 -
obs--98.8 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.42
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.362
LS refinement shell
*PLUS
Rfactor Rfree: 0.313 / % reflection Rfree: 5 % / Rfactor Rwork: 0.304 / Rfactor obs: 0.304

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