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- PDB-1kem: CATALYTIC ANTIBODY 28B4 FAB FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1kem
TitleCATALYTIC ANTIBODY 28B4 FAB FRAGMENT
Components(28B4 FAB) x 2
KeywordsCATALYTIC ANTIBODY / SULFIDE OXIDATION / MONOOXYGENASE / OXYGENATION / FAB / IMMUNOGLOBULIN
Function / homology
Function and homology information


phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding ...phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / cytoplasm
Similarity search - Function
: / 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 ...: / 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
: / Ig gamma-1 chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHsieh-Wilson, L.C. / Schultz, P.G. / Stevens, R.C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Insights into antibody catalysis: structure of an oxygenation catalyst at 1.9-angstrom resolution.
Authors: Hsieh-Wilson, L.C. / Schultz, P.G. / Stevens, R.C.
#1: Journal: J.Am.Chem.Soc. / Year: 1994
Title: An Efficient Antibody-Catalyzed Monooxygenation Reaction
Authors: Hsieh, L.C. / Stephans, J.C. / Schultz, P.G.
History
DepositionApr 16, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 28B4 FAB
H: 28B4 FAB


Theoretical massNumber of molelcules
Total (without water)47,3862
Polymers47,3862
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-22 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.200, 58.600, 43.400
Angle α, β, γ (deg.)95.30, 103.20, 93.60
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody 28B4 FAB


Mass: 23994.625 Da / Num. of mol.: 1 / Fragment: VARIABLE REGIONS OF LIGHT AND HEAVY CHAINS / Source method: isolated from a natural source
Details: THIS PROTEIN IS A FAB FRAGMENT PRODUCED UPON THE DIGESTION OF FULL-LENGTH MURINE MONOCLONAL ANTIBODY BY PAPAIN
Source: (natural) Mus musculus (house mouse) / Cell line: 28B4 / Strain: BALB/C / References: PIR: PC4203
#2: Antibody 28B4 FAB


Mass: 23391.201 Da / Num. of mol.: 1 / Fragment: VARIABLE REGIONS OF LIGHT AND HEAVY CHAINS / Source method: isolated from a natural source
Details: THIS PROTEIN IS A FAB FRAGMENT PRODUCED UPON THE DIGESTION OF FULL-LENGTH MURINE MONOCLONAL ANTIBODY BY PAPAIN
Source: (natural) Mus musculus (house mouse) / Cell line: 28B4 / Strain: BALB/C / References: UniProt: P01868
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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112.5 mg/mlFab1drop
210 mMTris-HCl1drop
3100 mM1dropNaCl
41 mMmethionine1drop
50.5 mMEDTA1drop
620 %PEG40001reservoir
710 %isopropanol1reservoir
80.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 21852 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.078
Reflection shellResolution: 2→2.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 8 / % possible all: 43
Reflection
*PLUS
Num. measured all: 51820
Reflection shell
*PLUS
% possible obs: 43 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / σ(F): 0
Details: RESIDUES SER H 126 - ALA H 135 DISPLAYED WEAK ELECTRON DENSITY AND ARE CONSIDERED DISORDERED IN THIS STRUCTURE.
RfactorNum. reflection% reflection
Rfree0.288 -10 %
Rwork0.183 --
obs0.183 21852 98 %
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 0 0 3335
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.875
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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