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- PDB-1g7m: CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH ... -

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Basic information

Entry
Database: PDB / ID: 1g7m
TitleCRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3 (VLW92V)
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
: / 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: 1.9 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 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

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


Theoretical massNumber of molelcules
Total (without water)38,8023
Polymers38,8023
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.67, 60.40, 56.79
Angle α, β, γ (deg.)90.00, 114.25, 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: 11613.898 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN / Mutation: W92V
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14% poly(ethylene glycol) 8000; 0.1 M sodium acetate; 0.05 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %(w/v)PEG80001reservoir
20.1 Msodium acetate1reservoir
30.05 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→99 Å / Num. all: 84329 / Num. obs: 27663 / % possible obs: 91.7 % / Rmerge(I) obs: 0.054
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.308 / % possible all: 87
Reflection
*PLUS
Num. measured all: 84329
Reflection shell
*PLUS
% possible obs: 87 %

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→15 Å
RfactorNum. reflection% reflection
Rfree0.2256 2545 9.2 %
Rwork0.1941 --
all-84329 -
obs-27663 91.7 %
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2706 0 0 116 2822
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.267
X-RAY DIFFRACTIONc_bond_d0.005
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 9.2 % / Rfactor obs: 0.1941
Solvent computation
*PLUS
Displacement parameters
*PLUS

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