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- PDB-6yoe: Structure of Lysozyme from SiN IMISX setup collected by still ser... -

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Basic information

Entry
Database: PDB / ID: 6yoe
TitleStructure of Lysozyme from SiN IMISX setup collected by still 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: 1.85 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)15,10811
Polymers14,3311
Non-polymers77710
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-9 kcal/mol
Surface area6940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.500, 78.500, 40.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-337-

HOH

21A-355-

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 , 5 types, 65 molecules

#2: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#3: Chemical
ChemComp-BR / BROMIDE ION


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


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


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.17 Å3/Da / Density % sol: 43.44 %
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: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→55.51 Å / Num. obs: 11247 / % possible obs: 100 % / Redundancy: 11.29 % / Biso Wilson estimate: 46.37 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.26 / Net I/σ(I): 2.3
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 1101 / CC1/2: 0.22 / Rrim(I) all: 1.2 / % possible all: 96.4
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
CrystFELdata scaling
PHENIX1.17.1_3660refinement
CrystFELdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D5F

5d5f


Resolution: 1.85→55.51 Å / SU ML: 0.3199 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.0566
RfactorNum. reflection% reflection
Rfree0.2846 563 5.01 %
Rwork0.2633 --
obs0.2644 11247 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.06 Å2
Refinement stepCycle: LAST / Resolution: 1.85→55.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 21 55 1076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261031
X-RAY DIFFRACTIONf_angle_d0.44481389
X-RAY DIFFRACTIONf_chiral_restr0.0372144
X-RAY DIFFRACTIONf_plane_restr0.0032181
X-RAY DIFFRACTIONf_dihedral_angle_d16.1881146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-2.040.39161360.32912584X-RAY DIFFRACTION99.52
2.04-2.330.32051390.2962630X-RAY DIFFRACTION99.93
2.33-2.940.29361390.32072666X-RAY DIFFRACTION99.96
2.94-55.510.27031490.23872804X-RAY DIFFRACTION99.83

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