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- PDB-2rcs: IMMUNOGLOBULIN 48G7 GERMLINE FAB-AFFINITY MATURATION OF AN ESTERO... -

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Basic information

Entry
Database: PDB / ID: 2rcs
TitleIMMUNOGLOBULIN 48G7 GERMLINE FAB-AFFINITY MATURATION OF AN ESTEROLYTIC ANTIBODY
Components(IMMUNOGLOBULIN 48G7 GERMLINE FAB) x 2
KeywordsGERMLINE ANTIBODY / FAB / CATALYTIC ANTIBODY / AFFINITY MATURATION
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / 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 / 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
: / 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 14, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: 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: IMMUNOGLOBULIN 48G7 GERMLINE FAB
H: IMMUNOGLOBULIN 48G7 GERMLINE FAB


Theoretical massNumber of molelcules
Total (without water)46,5282
Polymers46,5282
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-26 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.160, 75.550, 86.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody IMMUNOGLOBULIN 48G7 GERMLINE FAB


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 GERMLINE FAB


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
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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growpH: 6
Details: 10-15 MG/ML FAB IN 0.1M AMMONIUM ACETATE, 0.1M SODIUM CACODYLATE PH 6.0, 18% PEG 4000, 1% DIOXANE
Crystal grow
*PLUS
pH: 8 / 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
72.0 Mammonium sulfate1reservoir

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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: Jul 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: 27752 / % possible obs: 92.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 15.7
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 7.2 / Rsym value: 0.208 / % possible all: 91.2
Reflection
*PLUS
% possible obs: 97.3 % / Num. measured all: 94282 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 91.2 % / Rmerge(I) obs: 0.144

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GERMLINE FAB W HAPTEN

Resolution: 2.1→20 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.259 -10 %
Rwork0.21 --
obs0.21 23005 97.3 %
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4035 0 0 0 4035
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
Rfree0.258 -10 %
Rwork0.214 348 -
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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