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- PDB-1yqv: The crystal structure of the antibody Fab HyHEL5 complex with lys... -

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Basic information

Entry
Database: PDB / ID: 1yqv
TitleThe crystal structure of the antibody Fab HyHEL5 complex with lysozyme at 1.7A resolution
Components
  • Hen Egg White Lysozyme
  • HyHEL-5 Antibody Heavy Chain
  • HyHEL-5 Antibody Light Chain
KeywordsIMMUNE SYSTEM / HyHEL-5 ANTIBODY / lysozyme
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 speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCohen, G.H. / Silverton, E.W. / Padlan, E.A. / Dyda, F. / Wibbenmeyer, J.A. / Wilson, R.C. / Davies, D.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry.
Authors: Cohen, G.H. / Silverton, E.W. / Padlan, E.A. / Dyda, F. / Wibbenmeyer, J.A. / Willson, R.C. / Davies, D.R.
History
DepositionFeb 2, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionApr 26, 2005ID: 3HFL
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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
Remark 999SEQUENCE The sequence of HYHEL-5 light chain and heavy chain are not available at any of the ...SEQUENCE The sequence of HYHEL-5 light chain and heavy chain are not available at any of the sequence database at the time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: HyHEL-5 Antibody Light Chain
H: HyHEL-5 Antibody Heavy Chain
Y: Hen Egg White Lysozyme


Theoretical massNumber of molelcules
Total (without water)60,5883
Polymers60,5883
Non-polymers00
Water11,151619
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.459, 74.258, 78.256
Angle α, β, γ (deg.)90.00, 101.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody HyHEL-5 Antibody Light Chain


Mass: 23225.668 Da / Num. of mol.: 1 / Fragment: IG*G1 FAB FRAGMENT (HY/HEL-5) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C
#2: Antibody HyHEL-5 Antibody Heavy Chain


Mass: 23031.547 Da / Num. of mol.: 1 / Fragment: IG*G1 FAB FRAGMENT (HY/HEL-5) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C
#3: Protein Hen Egg White Lysozyme / 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) / Tissue: egg white / References: UniProt: P00698, lysozyme
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.91 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 66970 / Num. obs: 62951 / % possible obs: 94 % / Redundancy: 1.86 % / Net I/σ(I): 16.3

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Processing

Software
NameClassification
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HFL

3hfl
PDB Unreleased entry


Resolution: 1.7→30 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.234 3019 RANDOM
Rwork0.195 --
all-67180 -
obs-59847 -
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4273 0 0 619 4892
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_deg1.29
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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 shellHighest resolution: 1.7 Å
RfactorNum. reflection% reflection
Rfree0.234 3019 -
Rwork0.195 --
obs-59847 89.1 %

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