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- PDB-9fcc: HEN EGG-WHITE Lysozyme incubated at 80% relative humidity -

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Basic information

Entry
Database: PDB / ID: 9fcc
TitleHEN EGG-WHITE Lysozyme incubated at 80% relative humidity
ComponentsLysozyme C
KeywordsHYDROLASE / relative humidity
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsReinke, P.Y.A. / Guenther, S. / Falke, S. / Galchenkova, M. / Rahmani Mashhour, A. / Creon, A. / Lieske, J. / Ewert, W. / Rorigues, A.C. / Thekku Veedu, S. ...Reinke, P.Y.A. / Guenther, S. / Falke, S. / Galchenkova, M. / Rahmani Mashhour, A. / Creon, A. / Lieske, J. / Ewert, W. / Rorigues, A.C. / Thekku Veedu, S. / Fischer, P. / Meents, A.
Funding support Germany, 3items
OrganizationGrant numberCountry
Helmholtz AssociationFISCOV Germany
Helmholtz AssociationFRAGX Germany
Helmholtz AssociationHIR3X Germany
CitationJournal: To Be Published
Title: Exploring the conformational space of proteins by systematic variation of the relative humidity
Authors: Reinke, P.Y.A. / Meents, A.
History
DepositionMay 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5106
Polymers14,3311
Non-polymers1795
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-36 kcal/mol
Surface area6590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.479, 79.479, 37.886
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-363-

HOH

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Components

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


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1M NaCl, 35% (v/v) ethylene glycol, 20% (w/v) PEG4000, 50 mM sodium acetate pH 3.5

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: Humidity chamber controlled / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P09 HiPhaX / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.4→39.74 Å / Num. obs: 24447 / % possible obs: 99.89 % / Redundancy: 13.1 % / Biso Wilson estimate: 21.23 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 21.42
Reflection shellResolution: 1.4→1.45 Å / Mean I/σ(I) obs: 2.75 / Num. unique obs: 2357 / CC1/2: 0.852 / CC star: 0.959

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→39.74 Å / SU ML: 0.1462 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2219
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1836 2025 8.28 %
Rwork0.1508 22422 -
obs0.1535 24447 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.79 Å2
Refinement stepCycle: LAST / Resolution: 1.4→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 8 110 1119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841277
X-RAY DIFFRACTIONf_angle_d0.97241751
X-RAY DIFFRACTIONf_chiral_restr0.0788170
X-RAY DIFFRACTIONf_plane_restr0.0087246
X-RAY DIFFRACTIONf_dihedral_angle_d5.8308197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.2831370.27381529X-RAY DIFFRACTION98.58
1.44-1.470.24161400.22091579X-RAY DIFFRACTION100
1.47-1.520.21861440.20051586X-RAY DIFFRACTION100
1.52-1.570.2331390.18151561X-RAY DIFFRACTION100
1.57-1.620.2051500.17831583X-RAY DIFFRACTION100
1.62-1.690.19331320.18171583X-RAY DIFFRACTION100
1.69-1.760.22361550.17691579X-RAY DIFFRACTION100
1.76-1.860.19661360.1641600X-RAY DIFFRACTION100
1.86-1.970.15561520.14791588X-RAY DIFFRACTION100
1.97-2.130.17911440.13781597X-RAY DIFFRACTION100
2.13-2.340.16321440.13461613X-RAY DIFFRACTION100
2.34-2.680.15731420.13541634X-RAY DIFFRACTION100
2.68-3.370.19081530.14451637X-RAY DIFFRACTION100
3.37-39.740.18231570.14771753X-RAY DIFFRACTION99.95

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