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- PDB-8rus: Hen egg-white lysozyme (HEWL) structure from EuXFEL FXE, multi-hi... -

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Basic information

Entry
Database: PDB / ID: 8rus
TitleHen egg-white lysozyme (HEWL) structure from EuXFEL FXE, multi-hit Droplet-on-Demand (DoD) injection, 9.3 keV photon energy, space group P432121
ComponentsLysozyme C
KeywordsHYDROLASE / XFEL / Lysozyme / HEWL / EuXFEL / European XFEL / Droplet on Demand / Droplet-on-Demand / DoD / multihit / multi-hit / kilohertz / SFX / Serial
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 / DI(HYDROXYETHYL)ETHER / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsPerrett, S. / van Thor, J.J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Struct Dyn. / Year: 2024
Title: Kilohertz droplet-on-demand serial femtosecond crystallography at the European XFEL station FXE.
Authors: Perrett, S. / Fadini, A. / Hutchison, C.D.M. / Bhattacharya, S. / Morrison, C. / Turkot, O. / Jakobsen, M.B. / Grossler, M. / Licon-Salaiz, J. / Griese, F. / Flewett, S. / Valerio, J. / ...Authors: Perrett, S. / Fadini, A. / Hutchison, C.D.M. / Bhattacharya, S. / Morrison, C. / Turkot, O. / Jakobsen, M.B. / Grossler, M. / Licon-Salaiz, J. / Griese, F. / Flewett, S. / Valerio, J. / Schulz, J. / Biednov, M. / Jiang, Y. / Han, H. / Yousef, H. / Khakhulin, D. / Milne, C. / Barty, A. / van Thor, J.J.
History
DepositionJan 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)14,8389
Polymers14,3311
Non-polymers5078
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.470, 79.470, 38.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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: Canavalia ensiformis (jack bean) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 86 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 3.5
Details: 1:2 lysozyme (100 mg mL-1 in 50 mM NaOAc (pH 3.5)) and crystallization solution (0.1 M NaOAc (pH 3.5), 5% PEG6000 (v/v), 3.2 M NaCl) at 298K.

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: FXE / Wavelength: 1.333 Å
DetectorType: STFC Large Pixel Detector / Detector: PIXEL / Date: Nov 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.333 Å / Relative weight: 1
ReflectionResolution: 1.38→18.73 Å / Num. obs: 12383860 / % possible obs: 100 % / Redundancy: 479 % / Biso Wilson estimate: 35.6 Å2 / CC1/2: 0.99 / CC star: 0.997 / R split: 0.0836 / Net I/σ(I): 6.77
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 43 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 107809 / CC1/2: 0.01 / CC star: 0.134 / R split: 0.5488 / % possible all: 100
Serial crystallography measurementFocal spot size: 10 µm2 / Pulse duration: 50 fsec. / Pulse photon energy: 9290 keV / XFEL pulse repetition rate: 47000 Hz
Serial crystallography sample deliveryDescription: Droplet on Demand / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: PEG / Crystal conc.: 20000000 / Description: Droplet on Demand Multi Hit / Filter size: 20 µm / Injector diameter: 80 µm / Injector temperature: 298 K / Power by: piezoelectric
Serial crystallography data reductionFrames indexed: 74048 / Frames total: 255000 / XFEL run numbers: 3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→18.73 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 2639 10.24 %
Rwork0.1484 --
obs0.1535 25781 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→18.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 0 29 78 1103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d0.948
X-RAY DIFFRACTIONf_dihedral_angle_d9.206160
X-RAY DIFFRACTIONf_chiral_restr0.078151
X-RAY DIFFRACTIONf_plane_restr0.009191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.410.39351440.39551169X-RAY DIFFRACTION100
1.41-1.430.43071460.39841189X-RAY DIFFRACTION100
1.43-1.460.40111290.42111192X-RAY DIFFRACTION100
1.46-1.490.46071660.42711167X-RAY DIFFRACTION100
1.49-1.530.41591370.39851208X-RAY DIFFRACTION100
1.53-1.570.41261310.34871184X-RAY DIFFRACTION100
1.57-1.610.34181370.32051227X-RAY DIFFRACTION100
1.61-1.660.36061540.27561173X-RAY DIFFRACTION100
1.66-1.710.32951270.23591206X-RAY DIFFRACTION100
1.71-1.770.24841170.1871229X-RAY DIFFRACTION100
1.77-1.840.25281380.15551231X-RAY DIFFRACTION100
1.84-1.920.2561350.15171199X-RAY DIFFRACTION100
1.92-2.030.16651520.12051196X-RAY DIFFRACTION100
2.03-2.150.17791460.10011231X-RAY DIFFRACTION100
2.15-2.320.18381210.11421223X-RAY DIFFRACTION100
2.32-2.550.18111470.12621241X-RAY DIFFRACTION100
2.55-2.920.21451290.14151255X-RAY DIFFRACTION100
2.92-3.670.18711350.13291272X-RAY DIFFRACTION100
3.67-18.730.15421480.12531350X-RAY DIFFRACTION100

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