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- PDB-9p6r: Structure of lysozyme-N,N',N"-triacetylchitotriose complex determ... -

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Basic information

Entry
Database: PDB / ID: 9p6r
TitleStructure of lysozyme-N,N',N"-triacetylchitotriose complex determined using REyes for automated MicroED
ComponentsLysozyme C
KeywordsHYDROLASE / 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 / 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 / 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: 2.2 Å
AuthorsEremin, D. / Vlahakis, N.W. / Rodriguez, J.A. / Nelson, H.M.
Funding support United States, 5items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)HHMI-EPI United States
National Science Foundation (NSF, United States)CHE-1925607 United States
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)R01AT011990 United States
National Science Foundation (NSF, United States)DMR-1933487 United States
National Science Foundation (NSF, United States)CHE-2003418 United States
CitationJournal: J Am Chem Soc / Year: 2025
Title: Spatially Aware Diffraction Mapping Enables Fully Autonomous MicroED.
Authors: Dmitry B Eremin / Kunal K Jha / David A Delgadillo / Hongyu Zhang / Samuel H Foxman / Samuel N Johnson / Niko W Vlahakis / Duilio Cascio / Vincent Lavallo / Jose A Rodríguez / Hosea M Nelson /
Abstract: In the hands of experts, microcrystal electron diffraction (microED, a 3D ED method) is a powerful tool for structural chemistry and chemical discovery. To expand the accessibility and utility of ...In the hands of experts, microcrystal electron diffraction (microED, a 3D ED method) is a powerful tool for structural chemistry and chemical discovery. To expand the accessibility and utility of microED, we introduce Reciprocal Eyes (REyes), an autonomous and intelligent platform (available for academic use) that combines diffraction-based particle selection with real-time data processing to deliver crystal structures without human intervention. REyes spatially maps diffraction signal and autonomously selects crystallites of interest, relying on lattice-quality metrics to acquire and index high-resolution data sets from diverse compounds. Tested on four different transmission electron microscopes (TEMs), it consistently yields preliminary structural solutions from single crystallites of materials, peptides, metal complexes, natural products (NPs), and proteins.
History
DepositionJun 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 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)15,0174
Polymers14,3311
Non-polymers6863
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.570, 79.570, 39.830
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-305-

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 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 17 / 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-N,N',N"-triacetylchitotriose complex / Type: COMPLEX / 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
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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)
VitrificationCryogen name: ETHANE

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Data collection

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
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: 20 µm
Specimen holderTemperature (max): 100 K / Temperature (min): 100 K
Image recordingElectron dose: 0.09 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k)
ReflectionResolution: 2.2→50 Å / Num. obs: 6025 / % possible obs: 87.1 % / Rmerge(I) obs: 0.3
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 7.47 % / Num. measured obs: 723 / % possible all: 87.3

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Processing

EM softwareName: PHENIX / Category: 3D reconstruction
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 79.57 Å / B: 79.57 Å / C: 39.83 Å / Space group name: P43212 / Space group num: 96
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 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: 2.2→35.58 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 602 10.03 %
Rwork0.2376 --
obs0.2416 6004 87.23 %
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_d0.0081088
ELECTRON CRYSTALLOGRAPHYf_angle_d1.2371478
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d16.856191
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.068161
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.008190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.420.3581460.30631308ELECTRON CRYSTALLOGRAPHY88
2.42-2.770.31591480.29491335ELECTRON CRYSTALLOGRAPHY88
2.77-3.490.26931510.25381357ELECTRON CRYSTALLOGRAPHY88
3.49-35.580.23541570.17991402ELECTRON CRYSTALLOGRAPHY86

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