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- PDB-9fc8: HEN EGG-WHITE Lysozyme incubated at 60% relative humidity -

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Basic information

Entry
Database: PDB / ID: 9fc8
TitleHEN EGG-WHITE Lysozyme incubated at 60% 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)14,89113
Polymers14,3311
Non-polymers56012
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-41 kcal/mol
Surface area6770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.718, 79.718, 37.477
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-384-

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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / 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.: 106 / 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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5
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: 0.775 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: 0.775 Å / Relative weight: 1
ReflectionResolution: 1.4→21.68 Å / Num. obs: 24323 / % possible obs: 99.88 % / Redundancy: 25.9 % / Biso Wilson estimate: 21.11 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 17.7
Reflection shellResolution: 1.4→1.45 Å / Mean I/σ(I) obs: 1.18 / Num. unique obs: 2373 / CC1/2: 0.677 / CC star: 0.898

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→21.68 Å / SU ML: 0.1561 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4546
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1938 2015 8.29 %
Rwork0.1583 22305 -
obs0.1612 24320 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.94 Å2
Refinement stepCycle: LAST / Resolution: 1.4→21.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 30 106 1137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941276
X-RAY DIFFRACTIONf_angle_d1.04831735
X-RAY DIFFRACTIONf_chiral_restr0.0827168
X-RAY DIFFRACTIONf_plane_restr0.0111241
X-RAY DIFFRACTIONf_dihedral_angle_d14.3694486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.29071400.30241548X-RAY DIFFRACTION99.59
1.44-1.470.29931430.2611560X-RAY DIFFRACTION99.88
1.47-1.520.24421400.23251567X-RAY DIFFRACTION100
1.52-1.570.24281420.21541571X-RAY DIFFRACTION100
1.57-1.620.22921390.19761564X-RAY DIFFRACTION100
1.62-1.690.21961430.1921573X-RAY DIFFRACTION100
1.69-1.760.23361440.18481579X-RAY DIFFRACTION100
1.76-1.860.19751400.17321583X-RAY DIFFRACTION99.88
1.86-1.970.18591450.16061582X-RAY DIFFRACTION100
1.97-2.130.1831420.14591588X-RAY DIFFRACTION100
2.13-2.340.17951480.14161608X-RAY DIFFRACTION100
2.34-2.680.17311450.14011614X-RAY DIFFRACTION100
2.68-3.370.19221480.14491633X-RAY DIFFRACTION99.72
3.37-21.680.18711560.15221735X-RAY DIFFRACTION99.89

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