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- PDB-1aj7: IMMUNOGLOBULIN 48G7 GERMLINE FAB ANTIBODY COMPLEXED WITH HAPTEN 5... -

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Basic information

Entry
Database: PDB / ID: 1aj7
TitleIMMUNOGLOBULIN 48G7 GERMLINE FAB ANTIBODY COMPLEXED WITH HAPTEN 5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID. AFFINITY MATURATION OF AN ESTEROLYTIC ANTIBODY
Components
  • IMMUNOGLOBULIN 48G7 FAB (HEAVY CHAIN)
  • IMMUNOGLOBULIN 48G7 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN / GERMLINE ANTIBODY / FAB / CATALYTIC ANTIBODY / AFFINITY MATURATION
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
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-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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID / : / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWedemayer, G.J. / Wang, L.H. / Patten, P.A. / Schultz, P.G. / Stevens, R.C.
Citation
Journal: Science / Year: 1997
Title: Structural insights into the evolution of an antibody combining site.
Authors: Wedemayer, G.J. / Patten, P.A. / Wang, L.H. / Schultz, P.G. / Stevens, R.C.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: Crystal Structures of the Free and Liganded Form of an Esterolytic Catalytic Antibody
Authors: Wedemayer, G.J. / Wang, L.H. / Patten, P.A. / Schultz, P.G. / Stevens, R.C.
#2: Journal: Science / Year: 1996
Title: The Immunological Evolution of Catalysis
Authors: Patten, P.A. / Gray, N.S. / Yang, P.L. / Marks, C.B. / Wedemayer, G.J. / Boniface, J.J. / Stevens, R.C. / Schultz, P.G.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: A Genetic Approach to the Generation of Antibodies with Enhanced Catalytic Activities
Authors: Lesley, S.A. / Patten, P.A. / Schultz, P.G.
History
DepositionMay 15, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IMMUNOGLOBULIN 48G7 FAB (LIGHT CHAIN)
H: IMMUNOGLOBULIN 48G7 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8303
Polymers46,5282
Non-polymers3021
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-22 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.100, 60.900, 73.100
Angle α, β, γ (deg.)90.00, 104.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody IMMUNOGLOBULIN 48G7 FAB (LIGHT CHAIN)


Mass: 23464.988 Da / Num. of mol.: 1
Fragment: VARIABLE DOMAINS OF LIGHT AND HEAVY CHAINS AND CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: EACH CHAIN IS A FUSION POLYPEPTIDE WHICH IS PART HUMAN AND PART MOUSE
Cell line: 48G7 / Fragment: CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS / Plasmid: PSAL143 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 4768677
#2: Antibody IMMUNOGLOBULIN 48G7 FAB (HEAVY CHAIN)


Mass: 23062.750 Da / Num. of mol.: 1
Fragment: VARIABLE DOMAINS OF LIGHT AND HEAVY CHAINS AND CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: EACH CHAIN IS A FUSION POLYPEPTIDE WHICH IS PART HUMAN AND PART MOUSE
Cell line: 48G7 / Fragment: CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS / Plasmid: PSAL143 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01857
#3: Chemical ChemComp-NPE / 5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID


Mass: 302.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO7P

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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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growpH: 8
Details: 10-15 MG/ML FAB IN 100MM NACL, 10MM TRIS PH 8.0, 1MM METHIONINE, 1MM SODIUM AZIDE, 0.5 MM EDTA.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
2100 mM1dropNaCl
310 mMTris1drop
41 mMmethionine1drop
51 mMsodium azide1drop
60.5 mMEDTA1drop
70.1 Mammonium acetate1reservoir
80.1 Msodium cacodylate1reservoir
918 %PEG40001reservoir
101 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 23005 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 5.2 / Rsym value: 0.204 / % possible all: 98.1
Reflection
*PLUS
Num. measured all: 80267
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GAF

1gaf


Resolution: 2.1→20 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.258 -10 %
Rwork0.217 --
obs0.217 23005 99.5 %
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4035 0 32 0 4067
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_deg1.542
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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→2.11 Å / Total num. of bins used: 60
RfactorNum. reflection% reflection
Rfree0.286 35 10 %
Rwork0.233 339 -

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