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- PDB-8rlg: Perdeuterated hen egg-white lysozyme at room temperature -

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Basic information

Entry
Database: PDB / ID: 8rlg
TitlePerdeuterated hen egg-white lysozyme at room temperature
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / perdeuterated / room temperature
Function / homology
Function and homology information


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 ...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 / identical protein binding / cytoplasm
Similarity search - Function
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-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsRamos, J. / Laux, V. / Mason, S.A. / Lemee, M. / Bowler, M. / Diederichs, K. / Haertlein, M. / Forsyth, V.T. / Mossou, E. / Larsen, S. / Langkilde, A.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Structure and dynamics of the active site of hen egg-white lysozyme from atomic resolution neutron crystallography.
Authors: Ramos, J. / Laux, V. / Mason, S.A. / Lemee, M.H. / Bowler, M.W. / Diederichs, K. / Haertlein, M. / Forsyth, V.T. / Mossou, E. / Larsen, S. / Langkilde, A.E.
History
DepositionJan 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,00511
Polymers14,3881
Non-polymers61710
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint10 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.150, 31.760, 34.070
Angle α, β, γ (deg.)88.75, 71.71, 67.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14388.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.79 Å3/Da / Density % sol: 31.16 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.5
Details: 0.15 M sodium nitrate, 0.05 M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.07→21.53 Å / Num. obs: 43570 / % possible obs: 99.2 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.012 / Rrim(I) all: 0.043 / Net I/σ(I): 33.4
Reflection shellResolution: 1.07→1.11 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.225 / Num. unique obs: 4049 / CC1/2: 0.965 / Rpim(I) all: 0.09 / Rrim(I) all: 0.245 / % possible all: 92.9

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Processing

Software
NameClassification
SHELXrefinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→21.53 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1289 2179 5.2 %Random
Rwork0.0956 ---
obs-41391 99.2 %-
Refinement stepCycle: LAST / Resolution: 1.07→21.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1005 0 40 91 1136

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