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- PDB-3a6b: Crystal Structure of HyHEL-10 Fv mutant LN32D complexed with hen ... -

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Basic information

Entry
Database: PDB / ID: 3a6b
TitleCrystal Structure of HyHEL-10 Fv mutant LN32D 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 / MUTANT / IMMUNE SYSTEM-HYDROLASE COMPLEX / Allergen / Antimicrobial / Bacteriolytic enzyme / Disulfide bond / Glycosidase
Function / homology
Function and homology information


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 / defense response to Gram-positive bacterium ...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 / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYokota, A. / Tsumoto, K. / Shiroishi, M. / Nakanishi, T. / Kondo, H. / Kumagai, I.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme
Authors: Yokota, A. / Tsumoto, K. / Shiroishi, M. / Nakanishi, T. / Kondo, H. / Kumagai, I.
History
DepositionAug 28, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)38,7523
Polymers38,7523
Non-polymers00
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-10 kcal/mol
Surface area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.558, 56.558, 233.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11L-375-

HOH

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Components

#1: Antibody Lysozyme binding ig kappa chain V23-J2 region / light chain of lysozyme antibody hyhel-10


Mass: 11624.795 Da / Num. of mol.: 1 / Mutation: N32D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pKTN2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Antibody IG VH, anti-lysozyme / heavy chain of 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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


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.: 386 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE FOR CHAIN H IS FROM THE PRF DATABASE, ACCESSION CODE 1306354A. AND, THE AUTHORS ...THE SEQUENCE FOR CHAIN H IS FROM THE PRF DATABASE, ACCESSION CODE 1306354A. AND, THE AUTHORS BELIEVE THAT ALA114 IS CORRECT. CHAIN L IS N32D MUTANT.

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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: 2.41 Å3/Da / Density % sol: 48.96 %
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

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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: Oct 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→28.737 Å / Num. all: 36355 / Num. obs: 36331 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 14.1 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 6.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 14 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2.7 / Num. unique all: 5177 / Rsym value: 0.258 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C08

1c08


Resolution: 1.8→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2044519.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1780 5 %RANDOM
Rwork0.194 ---
obs0.194 35777 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.8232 Å2 / ksol: 0.507131 e/Å3
Displacement parametersBiso mean: 20.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 0 386 3107
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 277 4.8 %
Rwork0.237 5546 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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