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- PDB-2eiz: Crystal structure of humanized HYHEL-10 fv mutant(HW47Y)-hen lyso... -

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Basic information

Entry
Database: PDB / ID: 2eiz
TitleCrystal structure of humanized HYHEL-10 fv mutant(HW47Y)-hen lysozyme complex
Components
  • (ANTI-LYSOZYME ANTIBODY FV REGION) x 2
  • Lysozyme C
KeywordsIMMUNE SYSTEM/HYDROLASE / ANTIBODY / HYDROLASE / IMMUNE SYSTEM-HYDROLASE COMPLEX
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 speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionMar 14, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Derived calculations
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
Revision 1.4Oct 23, 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

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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)38,4473
Polymers38,4473
Non-polymers00
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1331.3 Å2
ΔGint-9.6 kcal/mol
Surface area10113.7 Å2
Unit cell
Length a, b, c (Å)97.100, 97.100, 76.822
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-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: 12488.860 Da / Num. of mol.: 1 / Fragment: VH FRAGMENT / Mutation: 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


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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, 47TH RESIDUE, TRP WAS ENGINEERED TO TYR.

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 28-31% PEGMME 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: 1.9→50 Å / Num. obs: 29501 / % possible obs: 99.7 % / Redundancy: 14.1 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.11
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.155 / Num. unique all: 2922 / % possible all: 100

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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 2DQJ

2dqj


Resolution: 1.9→19.67 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2149226.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1470 5 %RANDOM
Rwork0.214 ---
obs0.214 29415 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4189 Å2 / ksol: 0.420039 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--3.83 Å20 Å20 Å2
2---3.83 Å20 Å2
3---7.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 0 263 2963
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
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: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 234 4.8 %
Rwork0.222 4593 -
obs--99.8 %
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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