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- PDB-2yss: Crystal structure of Humanized HYHEL-10 FV mutant(HQ39KW47Y)-HEN ... -

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Basic information

Entry
Database: PDB / ID: 2yss
TitleCrystal structure of Humanized HYHEL-10 FV mutant(HQ39KW47Y)-HEN lysozyme complex
Components
  • (ANTI-LYSOZYME ANTIBODY FV REGION) x 2
  • Lysozyme C
KeywordsIMMUNE SYSTEM/HYDROLASE / IMMUNE SYSTEM / HYDROLASE / IMMUNE SYSTEM-HYDROLASE COMPLEX
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNakanishi, T. / Tsumoto, K. / Yokota, A. / Kondo, H. / Kumagai, I.
CitationJournal: Protein Sci. / Year: 2008
Title: Critical contribution of VH-VL interaction to reshaping of an antibody: the case of humanization of anti-lysozyme antibody, HyHEL-10
Authors: Nakanishi, T. / Tsumoto, K. / Yokota, A. / Kondo, H. / Kumagai, I.
History
DepositionApr 3, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_prop.value
Revision 1.3Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTI-LYSOZYME ANTIBODY FV REGION
B: ANTI-LYSOZYME ANTIBODY FV REGION
C: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)38,4483
Polymers38,4483
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-11 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.302, 73.933, 75.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody ANTI-LYSOZYME ANTIBODY FV REGION


Mass: 11626.876 Da / Num. of mol.: 1 / Fragment: VL FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRA / Production host: Escherichia coli (E. coli)
#2: Antibody ANTI-LYSOZYME ANTIBODY FV REGION


Mass: 12489.911 Da / Num. of mol.: 1 / Fragment: VH FRAGMENT / Mutation: Q39K/W47Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRA / Production host: Escherichia coli (E. coli)
#3: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d 4 / Gal d IV


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


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR ANTI- LYSOZYME ANTIBODY AT THE TIME OF PROCESSING. ...THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR ANTI- LYSOZYME ANTIBODY AT THE TIME OF PROCESSING. FOR VH FRAGMENT, 39TH RESIDUE, GLN AND 47TH RESIDUE, TRP WAS ENGINEERED TO LYS AND TYR, RESPECTIVELY.

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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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 28-31% PEG MME 550, 0.01M zinc sulfate, 0.1M MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 14041 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.138
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.344

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EIZ

2eiz


Resolution: 2.4→19.99 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1300807.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 693 5 %RANDOM
Rwork0.218 ---
obs0.218 13978 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.1344 Å2 / ksol: 0.389253 e/Å3
Displacement parametersBiso mean: 45.4 Å2
Baniso -1Baniso -2Baniso -3
1-10.31 Å20 Å20 Å2
2--8.48 Å20 Å2
3----18.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 0 36 2736
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 115 5.3 %
Rwork0.264 2072 -
obs--94.3 %
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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