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- PDB-1nbz: Crystal Structure of HyHEL-63 complexed with HEL mutant K97A -

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Basic information

Entry
Database: PDB / ID: 1nbz
TitleCrystal Structure of HyHEL-63 complexed with HEL mutant K97A
Components
  • Lysozyme C
  • antibody kappa light chain
  • immunoglobulin gamma 1 chain
KeywordsIMMUNE SYSTEM/HYDROLASE / antibody / lysozyme / mutant / IMMUNE SYSTEM-HYDROLASE COMPLEX
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / endosome to lysosome transport ...positive regulation of B cell activation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / endosome to lysosome transport / immunoglobulin complex, circulating / immunoglobulin receptor binding / antigen processing and presentation / positive regulation of endocytosis / immunoglobulin mediated immune response / complement activation, classical pathway / positive regulation of phagocytosis / antigen binding / multivesicular body / B cell differentiation / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / response to bacterium / positive regulation of immune response / cell wall macromolecule catabolic process / lysozyme / antibacterial humoral response / 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 / metal ion 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 / Immunoglobulin V-Type ...: / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Lysozyme / Immunoglobulin V-set domain / : / Lysozyme-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulin heavy constant gamma 2A / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMariuzza, R.A. / Li, Y. / Urrutia, M. / Smith-Gill, S.J.
CitationJournal: Biochemistry / Year: 2003
Title: Dissection of binding interactions in the complex between the anti-lysozyme antibody HyHEL-63 and its antigen
Authors: Li, Y. / Urrutia, M. / Smith-Gill, S.J. / Mariuzza, R.A.
History
DepositionDec 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
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_sheet.number_strands
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: antibody kappa light chain
B: immunoglobulin gamma 1 chain
C: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)60,4133
Polymers60,4133
Non-polymers00
Water9,314517
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.903, 90.903, 151.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Cell settingtetragonal
Space group name H-MP42212

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Components

#1: Antibody antibody kappa light chain


Mass: 23583.869 Da / Num. of mol.: 1 / Fragment: light chain
Source method: isolated from a genetically manipulated source
Details: first chain of Anti-Lysozyme Antibody HyHEL-63 / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: GenBank: 13359425, UniProt: P01837*PLUS
#2: Antibody immunoglobulin gamma 1 chain


Mass: 22556.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: second chain of Anti-Lysozyme Antibody HyHEL-63 / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P01865, UniProt: Q569W9*PLUS
#3: Protein Lysozyme C / E.C.3.2.1.17 / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d 4 / Gal d IV


Mass: 14273.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / 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.: 517 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, AMMONIUM ACETATE, SODIUM ACETATE, pH 4.60, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
215 %(w/v)PEG40001reservoir
30.1 Mammonium acetate1reservoir
40.05 Msodium acetate1reservoirpH4.6

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Data collection

Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→34.9 Å / Num. all: 42777 / Num. obs: 42777 / Observed criterion σ(I): 0 / Biso Wilson estimate: 10 Å2
Reflection
*PLUS
Num. obs: 472861 / % possible obs: 97.3 % / Num. measured all: 53340 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.92 Å / % possible obs: 93.2 % / Rmerge(I) obs: 0.366

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→34.9 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 357507.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 4306 10.1 %RANDOM
Rwork0.229 ---
obs0.2291 42777 78 %-
all-42777 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.3558 Å2 / ksol: 0.389196 e/Å3
Displacement parametersBiso mean: 20.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2--0.88 Å20 Å2
3----1.76 Å2
Refine analyzeLuzzati coordinate error free: 0.24 Å / Luzzati sigma a free: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.85→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4215 0 0 517 4732
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.392
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it2.112.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 601 9.8 %
Rwork0.268 5527 -
obs--68.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 9.6 % / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d0.022
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.82
LS refinement shell
*PLUS
Lowest resolution: 1.92 Å

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