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- PDB-6yod: Structure of Lysozyme from SiN IMISX setup collected by rotation ... -

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Basic information

Entry
Database: PDB / ID: 6yod
TitleStructure of Lysozyme from SiN IMISX setup collected by rotation serial crystallography on crystals prelocated by 2D X-ray phase-contrast imaging
ComponentsLysozyme
KeywordsHYDROLASE / 2D X-ray phase-contrast imaging / IMISX / in situ rotation images / prelocation / still images / serial crystallography
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
ACETIC ACID / 2-(2-ETHOXYETHOXY)ETHANOL / BROMIDE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsHuang, C.-Y. / Martiel, I. / Villanueva-Perez, P. / Panepucci, E. / Caffrey, M. / Wang, M.
CitationJournal: Iucrj / Year: 2020
Title: Low-dose in situ prelocation of protein microcrystals by 2D X-ray phase-contrast imaging for serial crystallography.
Authors: Martiel, I. / Huang, C.Y. / Villanueva-Perez, P. / Panepucci, E. / Basu, S. / Caffrey, M. / Pedrini, B. / Bunk, O. / Stampanoni, M. / Wang, M.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,22812
Polymers14,3311
Non-polymers89711
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-7 kcal/mol
Surface area6760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.990, 78.990, 38.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

21A-369-

HOH

31A-397-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 6 types, 110 molecules

#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#6: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.5
Details: 0.5-1 M NaBr, 50-100 mM CH3COONa, pH 4.5, and 15-30 %(v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→39.495 Å / Num. obs: 16419 / % possible obs: 99.87 % / Redundancy: 40.98 % / CC1/2: 0.99 / Rrim(I) all: 0.21 / Net I/σ(I): 13.58
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 36.73 % / Mean I/σ(I) obs: 0.86 / Num. unique obs: 1147 / CC1/2: 0.26 / Rrim(I) all: 12.17
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: IMISX / Sample dehydration prevention: SiN sandwich / Sample holding: SiN / Support base: 3D-printed holder in standard goniometer base

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_3494refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D5F

5d5f


Resolution: 1.601→39.495 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 23.5
RfactorNum. reflection% reflection
Rfree0.211 821 5 %
Rwork0.1893 --
obs0.1904 16419 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.26 Å2 / Biso mean: 32.6264 Å2 / Biso min: 20.3 Å2
Refinement stepCycle: final / Resolution: 1.601→39.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 29 99 1128
Biso mean--47.44 39.42 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.6014-1.70170.32281320.27222522
1.7017-1.83310.26991360.22122570
1.8331-2.01760.2341340.1782549
2.0176-2.30950.19941360.16052586
2.3095-2.90960.22361380.1962625
2.9096-39.4950.19361450.18742746

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