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- PDB-9ig6: Hen egg-white lysozyme structure determined by 3DED/MicroED on a ... -

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Basic information

Entry
Database: PDB / ID: 9ig6
TitleHen egg-white lysozyme structure determined by 3DED/MicroED on a 200 keV microscope
ComponentsLysozyme C
KeywordsHYDROLASE / 3DED / MicroED
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)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 2.8 Å
AuthorsShaikhqasem, A. / Hamdi, F. / Machner, L. / Parthier, C. / Breithaupt, C. / Kyrilis, F.L. / Feller, S.M. / Kastritis, P.L. / Stubbs, M.T.
Funding support6items
OrganizationGrant numberCountry
Other governmentBMBF ZIK HALOmem, grant no. 03Z22HN23
Other governmentBMBF ZIK HALOmem, grant no. 03Z22HI2
Other governmentBMBF, CORONAmem, grant no. 03COV04
Other governmentEFRE for Saxony-Anhalt (grant no. ZS/2016/04/78115 and grant no. ZS/2024/05/187255
Other governmentDFG, project numbers 391498659, RTG 2467 and 514901783, CRC 1664
Other governmentThe European Union Horizon Europe ERA Chair hot4cryo, project number 101086665
CitationJournal: To Be Published
Title: Hen egg-white lysozyme structure determined by 3DED/MicroED on a 200 keV microscope
Authors: Shaikhqasem, A. / Hamdi, F. / Machner, L. / Parthier, C. / Breithaupt, C. / Kyrilis, F.L. / Feller, S.M. / Kastritis, P.L. / Stubbs, M.T.
History
DepositionFeb 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 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


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.59, 78.59, 37.84
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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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 / Mutation: none / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cellular location: 129 / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: lysozyme / Type: TISSUE / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Gallus gallus (chicken)
Buffer solutionpH: 4.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K / Details: 12 seconds

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Data collection

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm
Image recordingElectron dose: 0.1 e/Å2 / Film or detector model: FEI CETA (4k x 4k)
EM diffraction shellResolution: 2.8→55.5 Å / Fourier space coverage: 80.7 % / Multiplicity: 7.7 / Num. of structure factors: 2574 / Phase residual: 58.6 °
EM diffraction statsFourier space coverage: 80.7 % / High resolution: 2.8 Å / Num. of intensities measured: 20009 / Num. of structure factors: 2574
Phase error rejection criteria: Weak reflections with I/sigma < 1.0 were excluded
Rmerge: 80

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
Image processingDetails: CRYSTALLOGRAPHY
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 78.6 Å / B: 78.6 Å / C: 37.8 Å / Space group name: P43212 / Space group num: 96
CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: OTHER
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3J4G

3j4g


Resolution: 2.8→25.765 Å / Cor.coef. Fo:Fc: 0.834 / Cor.coef. Fo:Fc free: 0.724 / Cross valid method: FREE R-VALUE
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.3261 129 5.025 %
Rwork0.2943 2438 -
all0.296 --
obs-2567 80.698 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.48 Å2
Baniso -1Baniso -2Baniso -3
1--4.552 Å20 Å20 Å2
2---4.552 Å20 Å2
3---9.103 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0040.0121021
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.3151.7771381
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg6.2395128
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg3.047511
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg14.82710166
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_6_deg14.4871050
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0980.2144
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0050.02819
ELECTRON CRYSTALLOGRAPHYr_nbd_refined0.2530.2509
ELECTRON CRYSTALLOGRAPHYr_nbtor_refined0.310.2698
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_refined0.450.250
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbd_refined0.20.224
ELECTRON CRYSTALLOGRAPHYr_symmetry_xyhbond_nbd_refined0.2790.211
ELECTRON CRYSTALLOGRAPHYr_mcbond_it2.4853.352515
ELECTRON CRYSTALLOGRAPHYr_mcangle_it4.1646.02642
ELECTRON CRYSTALLOGRAPHYr_scbond_it3.0293.772506
ELECTRON CRYSTALLOGRAPHYr_scangle_it4.9846.786739
ELECTRON CRYSTALLOGRAPHYr_lrange_it9.8341.3054456
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.801-2.8730.35890.3621610.3622150.8910.86579.06980.332
2.873-2.950.18650.3381730.3322230.9910.87179.82060.294
2.95-3.0350.19670.2961700.2912110.9520.90283.88630.261
3.035-3.1270.46780.3061660.3112120.7810.90182.07550.264
3.127-3.2280.23590.2641470.2622000.960.919780.22
3.228-3.3390.229100.251490.2491920.9530.92582.81250.204
3.339-3.4630.397100.2441540.2532010.9250.93581.5920.203
3.463-3.6020.2470.2231360.2241770.980.95180.7910.18
3.602-3.7580.372110.2621360.2711820.8580.93580.76920.217
3.758-3.9380.35840.2191310.2221650.9910.94581.81820.166
3.938-4.1450.54210.2451270.2471610.93579.50310.178
4.145-4.390.27570.231250.2331570.9220.94984.07640.185
4.39-4.6830.35570.2641060.2711460.9160.94577.39730.218
4.683-5.0440.17450.2811110.2751390.9960.92683.45320.199
5.044-5.5050.19430.3821020.3731360.9950.87877.20590.276
5.505-6.120.40240.328950.3311160.9210.89385.34480.248
6.12-7.0010.59880.394760.4131060.8430.87779.24530.298
7.001-8.420.33460.342720.341960.9040.88981.250.274
8.42-11.3190.33740.475610.466820.8620.81779.26830.359
11.319-25.7650.50240.569400.565570.350.82777.1930.445

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