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- PDB-1ic4: CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A)-HEN LYSOZYME COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ic4
TitleCRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A)-HEN LYSOZYME COMPLEX
Components
  • IGG1 FAB CHAIN H
  • LYSOZYME BINDING IG KAPPA CHAIN
  • LYSOZYME C
KeywordsPROTEIN BINDING/HYDROLASE / ANTIGEN-ANTIBODY COMPLEX / HYHEL-10 / ANTI-HEN EGG WHITE LYSOZYME ANTIBODY / PROTEIN BINDING-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 / adaptive immune response / 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 ...: / : / Lysozyme - #10 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Lysozyme C / Immunoglobulin kappa variable 5-48 / Ig heavy chain V region 36-60
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShiroishi, M. / Yokota, A. / Tsumoto, K. / Kondo, H. / Nishimiya, Y. / Horii, K. / Matsushima, M. / Ogasahara, K. / Yutani, K. / Kumagai, I.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex.
Authors: Shiroishi, M. / Yokota, A. / Tsumoto, K. / Kondo, H. / Nishimiya, Y. / Horii, K. / Matsushima, M. / Ogasahara, K. / Yutani, K. / Kumagai, I.
History
DepositionMar 30, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 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

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Assembly

Deposited unit
L: LYSOZYME BINDING IG KAPPA CHAIN
H: IGG1 FAB CHAIN H
Y: LYSOZYME C


Theoretical massNumber of molelcules
Total (without water)38,7073
Polymers38,7073
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.219, 57.219, 237.180
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 LYSOZYME BINDING IG KAPPA CHAIN


Mass: 11623.810 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01642
#2: Antibody IGG1 FAB CHAIN H


Mass: 12751.929 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-114 / Mutation: D32A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01823
#3: Protein LYSOZYME C


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.: 66 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: HEPES, MPD, PEG6000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown / PH range low: 7.8 / PH range high: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES11
29-11 %(w/v)PEG600011
37-9 %(w/v)MPD11

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 16, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 74484 / Num. obs: 17573 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.508 / % possible all: 94.9
Reflection
*PLUS
Num. measured all: 74484 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 96.1 % / Rmerge(I) obs: 0.318

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→8 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.279 1380 random
Rwork0.181 --
all0.184 74484 -
obs-13797 -
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 0 66 2784
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d2.7
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 2.7

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