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- PDB-1a2y: HEN EGG WHITE LYSOZYME, D18A MUTANT, IN COMPLEX WITH MOUSE MONOCL... -

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Basic information

Entry
Database: PDB / ID: 1a2y
TitleHEN EGG WHITE LYSOZYME, D18A MUTANT, IN COMPLEX WITH MOUSE MONOCLONAL ANTIBODY D1.3
Components
  • IGG1-KAPPA D1.3 FV (HEAVY CHAIN)
  • IGG1-KAPPA D1.3 FV (LIGHT CHAIN)
  • LYSOZYME
KeywordsCOMPLEX (IMMUNOGLOBULIN/HYDROLASE) / COMPLEX (IMMUNOGLOBULIN-HYDROLASE) / IMMUNOGLOBULIN V REGION / HYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME / EGG WHITE / COMPLEX (IMMUNOGLOBULIN-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 / 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 - #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 / 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
PHOSPHATE ION / Lysozyme C / Immunoglobulin kappa chain variable 12-41 / Ig heavy chain V region PJ14
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsTsuchiya, D. / Mariuzza, R.A.
Citation
Journal: Biochemistry / Year: 1998
Title: A mutational analysis of binding interactions in an antigen-antibody protein-protein complex.
Authors: Dall'Acqua, W. / Goldman, E.R. / Lin, W. / Teng, C. / Tsuchiya, D. / Li, H. / Ysern, X. / Braden, B.C. / Li, Y. / Smith-Gill, S.J. / Mariuzza, R.A.
#1: Journal: Biochemistry / Year: 1996
Title: Hydrogen Bonding and Solvent Structure in an Antigen-Antibody Interface. Crystal Structures and Thermodynamic Characterization of Three Fv Mutants Complexed with Lysozyme
Authors: Fields, B.A. / Goldbaum, F.A. / Dall'Acqua, W. / Malchiodi, E.L. / Cauerhff, A. / Schwarz, F.P. / Ysern, X. / Poljak, R.J. / Mariuzza, R.A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Bound Water Molecules and Conformational Stabilization Help Mediate an Antigen-Antibody Association
Authors: Bhat, T.N. / Bentley, G.A. / Boulot, G. / Greene, M.I. / Tello, D. / Dall'Acqua, W. / Souchon, H. / Schwarz, F.P. / Mariuzza, R.A. / Poljak, R.J.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: Solvent Rearrangement in an Antigen-Antibody Interface Introduced by Site-Directed Mutagenesis of the Antibody Combining Site
Authors: Ysern, X. / Fields, B.A. / Bhat, T.N. / Goldbaum, F.A. / Dall'Acqua, W. / Schwarz, F.P. / Poljak, R.J. / Mariuzza, R.A.
History
DepositionJan 13, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
A: IGG1-KAPPA D1.3 FV (LIGHT CHAIN)
B: IGG1-KAPPA D1.3 FV (HEAVY CHAIN)
C: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9404
Polymers38,8453
Non-polymers951
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-17 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.667, 61.212, 57.425
Angle α, β, γ (deg.)90.00, 119.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody IGG1-KAPPA D1.3 FV (LIGHT CHAIN)


Mass: 11700.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: EGG / Production host: Escherichia coli (E. coli) / References: UniProt: P01635
#2: Antibody IGG1-KAPPA D1.3 FV (HEAVY CHAIN)


Mass: 12857.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: EGG / Production host: Escherichia coli (E. coli) / References: UniProt: P01820
#3: Protein LYSOZYME


Mass: 14287.150 Da / Num. of mol.: 1 / Mutation: D18A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM (WHITE) / Organ: EGG / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00698, lysozyme
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 %(w/v)PEG80001reservoir
20.1 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Type: CHESS / Wavelength: 0.928
DetectorDetector: CCD / Date: Jul 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionHighest resolution: 1.5 Å / Num. obs: 59595 / % possible obs: 90.4 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.301 / % possible all: 30.1
Reflection
*PLUS
Num. measured all: 403840
Reflection shell
*PLUS
% possible obs: 50.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementStarting model: PDB ENTRY 1VFB

1vfb


Resolution: 1.5→7 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3416 6 %RANDOM
Rwork0.203 ---
obs0.203 56703 90.4 %-
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 5 485 3244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.49
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.35
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.5→1.55 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.308 208 3.3 %
Rwork0.302 2939 -
obs--50.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.35

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