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- PDB-2dqf: Crystal structure of hyhel-10 FV mutant (y33ay53a) complexed with... -

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Basic information

Entry
Database: PDB / ID: 2dqf
TitleCrystal structure of hyhel-10 FV mutant (y33ay53a) complexed with hen egg lysozyme
Components
  • Ig VH,anti-lysozyme
  • Lysozyme C
  • lysozyme binding Ig kappa chain V23-J2 region
KeywordsIMMUNE SYSTEM/HYDROLASE / ANTIGEN-ANTIBODY COMPLEX / MUTANT / IMMUNE SYSTEM-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 / RNA-directed DNA polymerase activity / cell wall macromolecule catabolic process / lysozyme ...immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / RNA-directed DNA polymerase 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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. ...: / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Ig heavy chain V region 36-60 / Anti-HIV-1 reverse transcriptase single-chain variable
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShiroishi, M. / Kondo, H. / Tsumoto, K. / Kumagai, I.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. The case of HyHEL-10-HEL
Authors: Shiroishi, M. / Tsumoto, K. / Tanaka, Y. / Yokota, A. / Nakanishi, T. / Kondo, H. / Kumagai, I.
History
DepositionMay 25, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 30, 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

Downloads & links

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Assembly

Deposited unit
A: lysozyme binding Ig kappa chain V23-J2 region
B: Ig VH,anti-lysozyme
C: Lysozyme C
D: lysozyme binding Ig kappa chain V23-J2 region
E: Ig VH,anti-lysozyme
F: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)77,1336
Polymers77,1336
Non-polymers00
Water2,846158
1
A: lysozyme binding Ig kappa chain V23-J2 region
B: Ig VH,anti-lysozyme
C: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)38,5673
Polymers38,5673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: lysozyme binding Ig kappa chain V23-J2 region
E: Ig VH,anti-lysozyme
F: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)38,5673
Polymers38,5673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.922, 98.922, 147.211
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody lysozyme binding Ig kappa chain V23-J2 region / light chain of lysozyme antibody hyhel-10


Mass: 11623.810 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PKTN2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q65ZI1*PLUS
#2: Antibody Ig VH,anti-lysozyme / heavy chain of lysozyme antibody hyhel-10


Mass: 12611.747 Da / Num. of mol.: 2 / Mutation: Y33A,Y53A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PKTN2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01823*PLUS
#3: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d 4 / Gal d IV


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: EGG WHITE / References: UniProt: P00698, lysozyme
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE FOR CHAIN B AND E IS FROM THE PRF DATABASE, ACCESSION CODE 1306354A. AND, THE AUTHORS ...THE SEQUENCE FOR CHAIN B AND E IS FROM THE PRF DATABASE, ACCESSION CODE 1306354A. AND, THE AUTHORS BELIEVE THAT ALA114 IS CORRECT. CHAIN B AND E IS ALSO TYR33ALA, TYR53ALA MUTANT.

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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: 2.67 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: AMMONIUM SULFATE, PEG4000, SODIUM ACETATE, pH 4.60, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→37 Å / Num. obs: 29457 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C08

1c08


Resolution: 2.5→8 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1424 -RANDOM
Rwork0.224 ---
obs0.224 28437 100 %-
Displacement parametersBiso mean: 43.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5414 0 0 158 5572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
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: 2.5→2.65 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.358 237 -
Rwork0.284 --
obs--99.9 %

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