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- PDB-1uac: Crystal Structure of HYHEL-10 FV MUTANT SFSF Complexed with TURKE... -

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Basic information

Entry
Database: PDB / ID: 1uac
TitleCrystal Structure of HYHEL-10 FV MUTANT SFSF Complexed with TURKEY WHITE LYSOZYME
Components
  • Ig VH,anti-lysozyme
  • Lysozyme C
  • lysozyme binding Ig kappa chain V23-J2 region
KeywordsIMMUNE SYSTEM/HYDROLASE / ANTIGEN-ANTIBODY COMPLEX / HYHEL-10 / MUTANT / ANTI-LYSOZYME ANTIBODY / IMMUNE SYSTEM-HYDROLASE COMPLEX
Function / homology
Function and homology information


glycosaminoglycan binding / 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 / 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)
Meleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKumagai, I. / Nishimiya, Y. / Kondo, H. / Tsumoto, K.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Structural consequences of target epitope-directed functional alteration of an antibody. The case of anti-hen lysozyme antibody, HyHEL-10
Authors: Kumagai, I. / Nishimiya, Y. / Kondo, H. / Tsumoto, K.
History
DepositionMar 8, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2004Provider: 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Nov 20, 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
L: lysozyme binding Ig kappa chain V23-J2 region
H: Ig VH,anti-lysozyme
Y: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)38,6163
Polymers38,6163
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.150, 67.150, 77.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Antibody lysozyme binding Ig kappa chain V23-J2 region / LYSOZYME ANTIBODY / HYHEL-10 VL


Mass: 11623.810 Da / Num. of mol.: 1
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: GenBank: 196585
#2: Antibody Ig VH,anti-lysozyme / LYSOZYME ANTIBODY / HYHEL-10 VH


Mass: 12763.939 Da / Num. of mol.: 1 / Mutation: Y53S, S54F, Y58F
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: PRF: 1306354A
#3: Protein Lysozyme C / C-TYPE LYSOZYME / HEN EGG WHITE LYSOZYME


Mass: 14228.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / Tissue: EGG WHITE / References: UniProt: P00703, lysozyme
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PEG 4000, ETHYLENE GLYCOL, AMMONIUM ACETATE, TRI-SODIUM CITRATE DEHYDRATE, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Kondo, H., (1999) J. Biol. Chem., 274, 27623.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-HCl1droppH7.5
2200 mM1dropNaCl
3200 mMammonium acetate1reservoir
4100 mMtri-sodium citrate dihydrate1reservoirpH6.6
520 %(w/v)PEG40001reservoir
610 %ethylene gylcol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 7, 1999 / Details: mirrors and monochromator
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 36020 / % possible obs: 96.7 % / Biso Wilson estimate: 16.655 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2 / Num. unique all: 5256 / % possible all: 95.2
Reflection
*PLUS
Lowest resolution: 20 Å / Redundancy: 3.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3430 -RANDOM
Rwork0.149 ---
obs0.149 -87.7 %-
all-33236 --
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 0 155 2867
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_from_restr_planes0.0277
X-RAY DIFFRACTIONs_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.047
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.028
X-RAY DIFFRACTIONs_chiral_restr0.04

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