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- PDB-9qum: Structure of lysozyme by continuous serial electron diffraction (... -

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Basic information

Entry
Database: PDB / ID: 9qum
TitleStructure of lysozyme by continuous serial electron diffraction (SerialED)
ComponentsLysozyme C
KeywordsHYDROLASE / serial electron diffraction / SerialED / lysozyme
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium / defense response to Gram-positive bacterium / endoplasmic reticulum / : / 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 / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 0.83 Å
AuthorsHofer, G. / Wang, L. / Pacoste, L. / Hager, P. / Fonjallaz, A. / Scaletti Hutchinson, E. / Stenmark, P. / Di Palma, M. / Williams, L. / Worral, J. ...Hofer, G. / Wang, L. / Pacoste, L. / Hager, P. / Fonjallaz, A. / Scaletti Hutchinson, E. / Stenmark, P. / Di Palma, M. / Williams, L. / Worral, J. / Steiner, R. / Xu, H. / Zou, X.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: Continuous Serial Electron Diffraction for High Quality Protein Structures
Authors: Hofer, G. / Wang, L. / Pacoste, L. / Hager, P. / Fonjallaz, A. / Williams, L. / Worrall, J. / Steiner, R. / Xu, H. / Zou, X.
History
DepositionApr 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: 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)16,4235
Polymers16,2581
Non-polymers1654
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-27 kcal/mol
Surface area6210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.660, 31.150, 33.570
Angle α, β, γ (deg.)87.730, 108.970, 111.600
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 16257.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Lysozyme / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.0162 MDa / Experimental value: NO
Source (natural)Organism: Gallus gallus (chicken)
Buffer solutionpH: 4.5
Details: Crystals were produced by adding 1 part of lysozyme solution (40 mg/mL) to 1 part of precipitant (0.8 M NaNO3, 50mM NaAc, pH 4.5)
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMsodium acetateNaAc1
20.8 Msodium nitrateNaNO31
SpecimenConc.: 40 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Hen egg white lysozyme
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationCryogen name: ETHANE
Details: Manual blotting in room temperature with ambient humidity

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Data collection

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / Calibrated defocus min: 0 nm / C2 aperture diameter: 20 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 98 K / Temperature (min): 78 K
Image recordingElectron dose: 1.52 e/Å2 / Film or detector model: FEI CETA (4k x 4k) / Details: FEI Ceta-D CMOS detector
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
2-11.731110055.99872916.36
0.83-0.852185.455.99766758.04
EM diffraction statsFourier space coverage: 99.9 % / High resolution: 0.83 Å / Num. of intensities measured: 5003763 / Num. of structure factors: 89374 / Phase error rejection criteria: 0 / Rmerge: 0.109
ReflectionBiso Wilson estimate: 8.7 Å2

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Processing

EM software
IDNameCategory
12PHENIX3D reconstruction
13PHENIXmodel refinement
EM 3D crystal entity∠α: 87.73 ° / ∠β: 108.97 ° / ∠γ: 111.6 ° / A: 26.66 Å / B: 31.15 Å / C: 33.57 Å / Space group name: P1 / Space group num: 1
CTF correctionType: NONE
3D reconstructionResolution: 0.83 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 11.04 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: maximum-likelihood
Atomic model buildingPDB-ID: 7SKW

7skw


Accession code: 7SKW / Source name: PDB / Type: experimental model
RefinementResolution: 0.83→11.73 Å / SU ML: 0.1562 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.8099
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 2000 2.28 %Random selection
Rwork0.1755 85855 --
obs0.1762 87855 98.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.04 Å2
Refinement stepCycle: LAST / Resolution: 0.83→11.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 7 147 1146
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.01881075
ELECTRON CRYSTALLOGRAPHYf_angle_d1.21951464
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.1137151
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0113196
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d6.3402161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.83-0.850.38231230.39425308ELECTRON CRYSTALLOGRAPHY85.43
0.85-0.870.40831370.39345842ELECTRON CRYSTALLOGRAPHY93.73
0.87-0.90.38721430.37196131ELECTRON CRYSTALLOGRAPHY98.03
0.9-0.930.33641440.34396195ELECTRON CRYSTALLOGRAPHY99.25
0.93-0.960.36641450.31936245ELECTRON CRYSTALLOGRAPHY99.75
0.96-10.30251450.28546218ELECTRON CRYSTALLOGRAPHY99.94
1-1.050.27561460.24616235ELECTRON CRYSTALLOGRAPHY99.98
1.05-1.10.25171440.20776211ELECTRON CRYSTALLOGRAPHY100
1.1-1.170.22721460.17366277ELECTRON CRYSTALLOGRAPHY100
1.17-1.260.19261450.15946248ELECTRON CRYSTALLOGRAPHY100
1.26-1.390.18431450.15366213ELECTRON CRYSTALLOGRAPHY100
1.39-1.590.20641470.14886260ELECTRON CRYSTALLOGRAPHY100
1.59-20.18091440.15526231ELECTRON CRYSTALLOGRAPHY100
2-11.730.15571460.13156241ELECTRON CRYSTALLOGRAPHY99.97

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