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- PDB-9os1: MicroED structure of lysozyme co-crystallized with N,N',N"-triace... -

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Entry
Database: PDB / ID: 9os1
TitleMicroED structure of lysozyme co-crystallized with N,N',N"-triacetylchitotriose
ComponentsLysozyme C
KeywordsHYDROLASE / Enzyme / ligand / complex / 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: 2.3 Å
AuthorsVlahakis, N.W. / Flowers, C.W. / Rodriguez, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)HHMI-EPI United States
National Science Foundation (NSF, United States)DMR-1548924 United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
CitationJournal: To Be Published
Title: Combining MicroED and native mass spectrometry for structural discovery of enzyme-small molecule complexes
Authors: Vlahakis, N.W. / Flowers, C.W. / Liu, M. / Agdanowski, M. / Johnson, S. / Summers, J.A. / Jacobs, L.M.C. / Keyser, C. / Russell, P. / Rose, S. / Orlans, J. / Adhami, N. / Chen, Y. / Sawaya, ...Authors: Vlahakis, N.W. / Flowers, C.W. / Liu, M. / Agdanowski, M. / Johnson, S. / Summers, J.A. / Jacobs, L.M.C. / Keyser, C. / Russell, P. / Rose, S. / Orlans, J. / Adhami, N. / Chen, Y. / Sawaya, M.R. / Basu, S. / De Sanctis, D. / Chen, Y. / Wakatsuki, S. / Nelson, H.M. / Loo, J. / Tang, Y. / Rodriguez, J.A.
History
DepositionMay 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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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)14,9823
Polymers14,3311
Non-polymers6512
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.150, 77.150, 37.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Fragment: lyzozyme / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 627.594 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Lysozyme bound to N,N',N"-triacetylchitotriose / Type: COMPLEX
Details: Crystals formed by vapor diffusion in sitting drops, from 80 mg/mL lysozyme mixed 1:1 with reservoir solution (800 mM NaCl, 80 mM sodium acetate pH 4.8)
Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Gallus gallus (chicken)
EM crystal formationDetails: Crystals formed by vapor diffusion in sitting drops, from 80 mg/mL lysozyme mixed 1:1 with reservoir solution (800 mM NaCl, 80 mM sodium acetate pH 4.8)
Temperature: 293 K
Buffer solutionpH: 4.8 / Details: 800 mM NaCl, 80 mM sodium acetate pH 4.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: TFS TALOS F200C
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 / C2 aperture diameter: 70 µm
Image recordingElectron dose: 0.09 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k)
EM diffraction shellResolution: 2.3→2.4 Å / Fourier space coverage: 88.6 % / Multiplicity: 8.8 / Num. of structure factors: 562 / Phase residual: 35.2 °
EM diffraction statsFourier space coverage: 87.5 % / High resolution: 2.3 Å / Num. of intensities measured: 40130 / Num. of structure factors: 4738 / Phase error rejection criteria: NONE / Rmerge: 0.283

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 77.15 Å / B: 77.15 Å / C: 37.49 Å / Space group name: P43212 / Space group num: 96
CTF correctionType: NONE
3D reconstructionResolution: 2.3 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingPDB-ID: 1DPX

1dpx


Accession code: 1DPX / Source name: PDB / Type: experimental model
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→34.5 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 473 10.03 %
Rwork0.2246 --
obs0.2283 4718 87.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0071070
ELECTRON CRYSTALLOGRAPHYf_angle_d1.2311452
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d18.644187
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.073160
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.009185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.630.33031530.29991380ELECTRON CRYSTALLOGRAPHY88
2.63-3.320.29371570.28061404ELECTRON CRYSTALLOGRAPHY88
3.32-34.50.23211630.18061461ELECTRON CRYSTALLOGRAPHY87

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