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- PDB-1j1o: Crystal Structure of HyHEL-10 Fv mutant LY50F complexed with hen ... -

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Basic information

Entry
Database: PDB / ID: 1j1o
TitleCrystal Structure of HyHEL-10 Fv mutant LY50F complexed with hen egg white lysozyme
Components
  • Ig VH,anti-lysozyme
  • Lysozyme C
  • lysozyme binding Ig kappa chain V23-J2 region
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 / adaptive immune response / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYokota, A. / Tsumoto, K. / Shiroishi, M. / Kondo, H. / Kumagai, I.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: The Role of Hydrogen Bonding via Interfacial Water Molecules in Antigen-Antibody Complexation. THE HyHEL-10-HEL INTERACTION
Authors: Yokota, A. / Tsumoto, K. / Shiroishi, M. / Kondo, H. / Kumagai, I.
History
DepositionDec 13, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: lysozyme binding Ig kappa chain V23-J2 region
H: Ig VH,anti-lysozyme
Y: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)38,7353
Polymers38,7353
Non-polymers00
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-12 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.230, 56.230, 234.486
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 lysozyme binding Ig kappa chain V23-J2 region / Lysozyme Antibody / HyHEL-10


Mass: 11607.810 Da / Num. of mol.: 1 / Mutation: Y50F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pKTN2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01642
#2: Antibody Ig VH,anti-lysozyme / Lysozyme Antibody / HyHEL-10


Mass: 12795.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pKTN2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01823
#3: Protein Lysozyme C


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


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.16 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: PEG 6000, Hepes, glycerol, methyl-pentanediol, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Kondo, H., (1999) J.Biol.Chem., 274, 27623. / PH range low: 7.8 / PH range high: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMHEPES1reservoirpH7.6-7.8
29-11 %(w/v)PEG60001reservoir
315 %glycerol1reservoir
47-9 %(w/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→29.3 Å / Num. all: 36032 / Num. obs: 35999 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 19.285 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.059 / Net I/σ(I): 8.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5161 / Rsym value: 0.232 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 1760 5 %random
Rwork0.19 ---
all-35643 --
obs-35406 --
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2720 0 0 343 3063
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.29
LS refinement shellResolution: 1.8→1.82 Å
RfactorNum. reflection
Rfree0.2253 58
Rwork0.2386 -
obs-1012
Refinement
*PLUS
Rfactor Rfree: 0.215 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.004399

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