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- PDB-8jqv: Hen egg-white lysozyme solved from 1D fixed target delivery system -

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Basic information

Entry
Database: PDB / ID: 8jqv
TitleHen egg-white lysozyme solved from 1D fixed target delivery system
ComponentsLysozyme C
KeywordsHYDROLASE / glycan hydrolase
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)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsKim, J. / Park, S. / Park, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029733 Korea, Republic Of
CitationJournal: Photonics / Year: 2024
Title: Application of Micro-Tubing Reeling System to Serial Femtosecond Crystallography
Authors: Kim, J. / Park, S. / Cho, Y. / Park, J.
History
DepositionJun 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 30, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_id_ISSN

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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
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.300, 79.300, 38.300
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 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4 / Details: 0.1M sodium acetate pH4.0, 2M NaCl, 5% PEG 6K

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Apr 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 12462 / % possible obs: 100 % / Redundancy: 340.7 % / Biso Wilson estimate: 32.17 Å2 / CC1/2: 0.91 / CC star: 0.97 / R split: 0.25 / Net I/σ(I): 3.73
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 237.1 % / Mean I/σ(I) obs: 1.59 / Num. unique obs: 1150 / CC1/2: 0.42 / CC star: 0.78 / R split: 0.69 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→39.65 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 736 6.23 %
Rwork0.204 --
obs0.2056 11807 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 72 1073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061021
X-RAY DIFFRACTIONf_angle_d0.8791381
X-RAY DIFFRACTIONf_dihedral_angle_d5.938143
X-RAY DIFFRACTIONf_chiral_restr0.054144
X-RAY DIFFRACTIONf_plane_restr0.01181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.940.39111440.37722167X-RAY DIFFRACTION100
1.94-2.130.26541440.21872163X-RAY DIFFRACTION100
2.13-2.440.25561450.21512182X-RAY DIFFRACTION100
2.44-3.080.23771470.20962211X-RAY DIFFRACTION100
3.08-39.650.19481560.17942348X-RAY DIFFRACTION100

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