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- PDB-1p2c: crystal structure analysis of an anti-lysozyme antibody -

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Basic information

Entry
Database: PDB / ID: 1p2c
Titlecrystal structure analysis of an anti-lysozyme antibody
Components
  • Lysozyme C
  • heavy chain VH+CH1 anti-lysozyme antibody F10.6.6
  • light chain anti-lysozyme antibody F10.6.6
KeywordsIMMUNE SYSTEM/HYDROLASE / monoclonal antibody IgG1 / kappa antibody-antigen complex / IMMUNE SYSTEM-HYDROLASE COMPLEX
Function / homology
Function and homology information


humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding ...humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / positive regulation of immune response / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / antibacterial humoral response / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / external side of plasma membrane / endoplasmic reticulum / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Lysozyme C / Immunoglobulin kappa constant / Ig gamma-1 chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCauerhff, A. / Goldbaum, F.A. / Braden, B.C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural mechanism for affinity maturation of an anti-lysozyme antibody.
Authors: Cauerhff, A. / Goldbaum, F.A. / Braden, B.C.
#1: Journal: J.Immunol. / Year: 1999
Title: Lack of significant differences in association rates and affinities of antibodies from short-term and long-term responses to hen egg lysozyme
Authors: Goldbaum, F.A. / Cauerhff, A. / Velikovsky, C.A. / Llera, A.S. / Riottot, M.M. / Poljak, R.J.
History
DepositionApr 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THERE IS NO APPROPRIATE SEQUENCE DATABASE MATCH FOR THE ANTIBODY CHAINS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: light chain anti-lysozyme antibody F10.6.6
B: heavy chain VH+CH1 anti-lysozyme antibody F10.6.6
C: Lysozyme C
D: light chain anti-lysozyme antibody F10.6.6
E: heavy chain VH+CH1 anti-lysozyme antibody F10.6.6
F: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)122,1386
Polymers122,1386
Non-polymers00
Water15,979887
1
A: light chain anti-lysozyme antibody F10.6.6
B: heavy chain VH+CH1 anti-lysozyme antibody F10.6.6
C: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)61,0693
Polymers61,0693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: light chain anti-lysozyme antibody F10.6.6
E: heavy chain VH+CH1 anti-lysozyme antibody F10.6.6
F: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)61,0693
Polymers61,0693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.660, 73.750, 83.780
Angle α, β, γ (deg.)66.59, 74.74, 85.44
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is an Fab fragment (light chain+VH and CH1 domains) bound to a hen egg-white lysozyme

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Components

#1: Antibody light chain anti-lysozyme antibody F10.6.6


Mass: 23320.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C / References: UniProt: P01837*PLUS
#2: Antibody heavy chain VH+CH1 anti-lysozyme antibody F10.6.6


Mass: 23417.127 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C / References: UniProt: P01868*PLUS
#3: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d 4 / Gal d IV


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 887 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: PEG 1000, CaCl2, pH 4.6, vapor diffusion, temperature 298.K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
25 mMTris1droppH7.5
328 %PEG10001reservoir
40.2 M1reservoirpH4.6CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 10, 2002 / Details: confocal mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionLowest resolution: 2 Å / Num. obs: 60488 / % possible obs: 95 % / Rmerge(I) obs: 0.013
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.036
Reflection
*PLUS
Highest resolution: 2 Å

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CrystalClear(MSC/RIGAKU)data reduction
CNSrefinement
CrystalClear(MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D44.1 Fab

Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.242 6099 random
Rwork0.204 --
obs-60226 -
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8463 0 0 887 9350
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.006
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.395

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