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- PDB-1c08: CRYSTAL STRUCTURE OF HYHEL-10 FV-HEN LYSOZYME COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1c08
TitleCRYSTAL STRUCTURE OF HYHEL-10 FV-HEN LYSOZYME COMPLEX
Components
  • (ANTI-HEN EGG WHITE LYSOZYME ANTIBODY (HYHEL-10)) x 2
  • LYSOZYME
KeywordsIMMUNE SYSTEM/HYDROLASE / ANTIGEN-ANTIBODY COMPLEX / IMMUNE SYSTEM-HYDROLASE COMPLEX
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / adaptive immune response / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
: / : / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family ...: / : / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Immunoglobulin V-set domain / Lysozyme / Lysozyme-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / 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 variable 5-48 / Ig heavy chain V region 36-60
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsShiroishi, M. / Kondo, H. / Matsushima, M. / Tsumoto, K. / Kumagai, I.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Crystal structure of anti-Hen egg white lysozyme antibody (HyHEL-10) Fv-antigen complex. Local structural changes in the protein antigen and water-mediated interactions of Fv-antigen and light ...Title: Crystal structure of anti-Hen egg white lysozyme antibody (HyHEL-10) Fv-antigen complex. Local structural changes in the protein antigen and water-mediated interactions of Fv-antigen and light chain-heavy chain interfaces.
Authors: Kondo, H. / Shiroishi, M. / Matsushima, M. / Tsumoto, K. / Kumagai, I.
History
DepositionJul 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 31, 2023Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQEUNCE THE SEQUENCE FOR CHAIN H IS FROM THE PRF DATABASE ACCESSION CODE 1306354A THE AUTHORS ...SEQEUNCE THE SEQUENCE FOR CHAIN H IS FROM THE PRF DATABASE ACCESSION CODE 1306354A THE AUTHORS BELIEVE THAT ALA114 IS CORRECT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTI-HEN EGG WHITE LYSOZYME ANTIBODY (HYHEL-10)
B: ANTI-HEN EGG WHITE LYSOZYME ANTIBODY (HYHEL-10)
C: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)38,7513
Polymers38,7513
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.208, 57.208, 236.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody ANTI-HEN EGG WHITE LYSOZYME ANTIBODY (HYHEL-10)


Mass: 11623.810 Da / Num. of mol.: 1 / Fragment: VL FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PKTN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01642
#2: Antibody ANTI-HEN EGG WHITE LYSOZYME ANTIBODY (HYHEL-10)


Mass: 12795.939 Da / Num. of mol.: 1 / Fragment: VH FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PKTN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01823
#3: Protein LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: HEPES, PEG6000, MPD, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / PH range low: 7.8 / PH range high: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES1reservoir
29-11 %(w/v)PEG60001reservoir
37-9 %(w/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Sep 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→8 Å / Num. all: 146870 / Num. obs: 18301 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 8 % / Rmerge(I) obs: 0.265 / Num. unique all: 1771 / % possible all: 97.6
Reflection shell
*PLUS
% possible obs: 97.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementResolution: 2.3→8 Å / σ(F): 0 / Details: Program X-PLOR by Brunger was also used.
RfactorNum. reflection% reflectionSelection details
Rfree0.175 915 -Reflection data chosen randomly from 5.0% of the observed data were used.
Rwork0.235 ---
all0.175 146870 --
obs-18301 98.5 %-
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 0 125 2846
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d2.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.235 / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS

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