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- PDB-1g7i: CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH ... -

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Basic information

Entry
Database: PDB / ID: 1g7i
TitleCRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3 (VLW92F)
Components
  • (ANTI-HEN EGG WHITE LYSOZYME MONOCLONAL ANTIBODY D1.3) x 2
  • LYSOZYME C
KeywordsHYDROLASE INHIBITOR/HYDROLASE / HYDROLASE INHIBITOR-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
PHOSPHATE ION / : / Lysozyme C / Ig heavy chain V region PJ14
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSundberg, E.J. / Urrutia, M. / Braden, B.C. / Isern, J. / Mariuzza, R.A.
CitationJournal: Biochemistry / Year: 2000
Title: Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface.
Authors: Sundberg, E.J. / Urrutia, M. / Braden, B.C. / Isern, J. / Tsuchiya, D. / Fields, B.A. / Malchiodi, E.L. / Tormo, J. / Schwarz, F.P. / Mariuzza, R.A.
History
DepositionNov 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 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 1.5Oct 9, 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: ANTI-HEN EGG WHITE LYSOZYME MONOCLONAL ANTIBODY D1.3
B: ANTI-HEN EGG WHITE LYSOZYME MONOCLONAL ANTIBODY D1.3
C: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9454
Polymers38,8503
Non-polymers951
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.270, 59.150, 56.080
Angle α, β, γ (deg.)90.00, 119.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody ANTI-HEN EGG WHITE LYSOZYME MONOCLONAL ANTIBODY D1.3


Mass: 11661.941 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN / Mutation: W92F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 1333979
#2: Antibody ANTI-HEN EGG WHITE LYSOZYME MONOCLONAL ANTIBODY D1.3


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


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: 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.: 398 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15-18%poly(ethylene glycol) 8000; 0.1 M potassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: used macroseeding / 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

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→500 Å / Num. obs: 30405 / % possible obs: 98.3 %
Reflection shellResolution: 1.8→1.86 Å / % possible all: 82.6

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→15 Å
RfactorNum. reflection% reflection
Rfree0.2476 2158 7.1 %
Rwork0.1878 --
obs-30405 98.3 %
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 5 398 3141
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.631
X-RAY DIFFRACTIONc_bond_d0.009
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 7.1 % / Rfactor obs: 0.1828
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg

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