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- PDB-1kir: FV MUTANT Y(A 50)S (VL DOMAIN) OF MOUSE MONOCLONAL ANTIBODY D1.3 ... -

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Basic information

Entry
Database: PDB / ID: 1kir
TitleFV MUTANT Y(A 50)S (VL DOMAIN) OF MOUSE MONOCLONAL ANTIBODY D1.3 COMPLEXED WITH HEN EGG WHITE LYSOZYME
Components
  • (MONOCLONAL ANTIBODY D1.3) x 2
  • LYSOZYME
KeywordsCOMPLEX (IMMUNOGLOBULIN/HYDROLASE) / IMMUNOGLOBULIN V REGION / HYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME / EGG WHITE / COMPLEX (IMMUNOGLOBULIN-HYDROLASE) / 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 / 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 / Immunoglobulin V-Type ...: / 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 / 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
: / : / Lysozyme C / Ig heavy chain V region PJ14
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsFields, B.A. / Poljak, R.J. / Mariuzza, R.A.
Citation
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.
#1: 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.
#2: 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
DepositionOct 23, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Structure summary / Category: 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: MONOCLONAL ANTIBODY D1.3
B: MONOCLONAL ANTIBODY D1.3
C: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)38,8133
Polymers38,8133
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.220, 60.450, 56.770
Angle α, β, γ (deg.)90.00, 119.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody MONOCLONAL ANTIBODY D1.3


Mass: 11624.881 Da / Num. of mol.: 1 / Mutation: Y(A 50)S (VL DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: EGG / Production host: Escherichia coli (E. coli) / References: GenBank: 554121
#2: Antibody MONOCLONAL ANTIBODY D1.3


Mass: 12857.275 Da / Num. of mol.: 1 / Mutation: Y(A 50)S (VL DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: EGG / Production host: Escherichia coli (E. coli) / References: GenBank: 896294, UniProt: P01820*PLUS
#3: Protein LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cell: EGG / Cellular location: EGG WHITE / Organ: EGG / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding / PH range low: 6.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-18 %(w/v)PEG80001reservoir
20.1 Mpotassium phosphate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 8, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 21066 / % possible obs: 82.8 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.082
Reflection
*PLUS
Num. measured all: 47313

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata scaling
X-PLOR3.1phasing
RefinementResolution: 2→7 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.167 --
obs0.167 16783 66.1 %
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 0 142 2867
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.91

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