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- PDB-1dqj: CRYSTAL STRUCTURE OF THE ANTI-LYSOZYME ANTIBODY HYHEL-63 COMPLEXE... -

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Basic information

Entry
Database: PDB / ID: 1dqj
TitleCRYSTAL STRUCTURE OF THE ANTI-LYSOZYME ANTIBODY HYHEL-63 COMPLEXED WITH HEN EGG WHITE LYSOZYME
Components
  • ANTI-LYSOZYME ANTIBODY HYHEL-63 (HEAVY CHAIN)
  • ANTI-LYSOZYME ANTIBODY HYHEL-63 (LIGHT CHAIN)
  • LYSOZYME
Keywordsimmune system/hydrolase / antibody / protein-protein complex / hen egg white lysozyme / immune system-hydrolase COMPLEX
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / 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 / endosome to lysosome transport ...positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / 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 / endosome to lysosome transport / antigen processing and presentation / immunoglobulin mediated immune response / regulation of proteolysis / positive regulation of endocytosis / complement activation, classical pathway / antigen binding / multivesicular body / Lactose synthesis / Antimicrobial peptides / positive regulation of phagocytosis / B cell differentiation / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / response to bacterium / positive regulation of immune response / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / 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 - #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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Lysozyme C / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 2A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLi, H. / Mariuzza, R.A.
CitationJournal: Biochemistry / Year: 2000
Title: Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,).
Authors: Li, Y. / Li, H. / Smith-Gill, S.J. / Mariuzza, R.A.
History
DepositionJan 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 7, 2021Group: Data collection / Refinement description / Category: refine / reflns
Item: _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs ..._refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _reflns.number_all / _reflns.number_obs
Revision 1.4Nov 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTI-LYSOZYME ANTIBODY HYHEL-63 (LIGHT CHAIN)
B: ANTI-LYSOZYME ANTIBODY HYHEL-63 (HEAVY CHAIN)
C: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)60,4713
Polymers60,4713
Non-polymers00
Water8,413467
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.58, 90.58, 150.06
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

21B-222-

HOH

31B-223-

HOH

DetailsThe biological assembly is a heterodimer with heavy and light chains

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Components

#1: Antibody ANTI-LYSOZYME ANTIBODY HYHEL-63 (LIGHT CHAIN)


Mass: 23583.869 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: GenBank: 2950241, UniProt: P01837*PLUS
#2: Antibody ANTI-LYSOZYME ANTIBODY HYHEL-63 (HEAVY CHAIN)


Mass: 22556.023 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P01865*PLUS
#3: Protein LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM / Plasmid: PPIC9 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00698, lysozyme
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4K, Ammonium acetate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
215 %(w/v)PEG40001reservoir
30.1 Mammonium acetate1reservoir
40.05 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 45762 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 19.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.371 / % possible all: 85
Reflection
*PLUS
Num. obs: 45762 / Num. measured all: 366760
Reflection shell
*PLUS
% possible obs: 85 % / Mean I/σ(I) obs: 5.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2→100 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1946 4.9 %RANDOM
Rwork0.217 ---
all0.217 45762 --
obs0.217 39827 92 %-
Refinement stepCycle: LAST / Resolution: 2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 0 467 4793
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.005
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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