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- PDB-8sil: Lysozyme crystallized in cyclic olefin copolymer-based microfluid... -

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Basic information

Entry
Database: PDB / ID: 8sil
TitleLysozyme crystallized in cyclic olefin copolymer-based microfluidic chips
ComponentsLysozyme C
KeywordsHYDROLASE / Hen Egg-White
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: 1.7 Å
AuthorsLiu, Z. / Gu, K. / Shelby, M.L. / Gilbile, D. / Lyubimov, A.Y. / Russi, S. / Cohen, A.E. / Coleman, M.A. / Frank, M. / Kuhl, T.L. ...Liu, Z. / Gu, K. / Shelby, M.L. / Gilbile, D. / Lyubimov, A.Y. / Russi, S. / Cohen, A.E. / Coleman, M.A. / Frank, M. / Kuhl, T.L. / Botha, S. / Poitevin, F. / Sierra, R.G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Department of Energy (DOE, United States) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography.
Authors: Liu, Z. / Gu, K.K. / Shelby, M.L. / Gilbile, D. / Lyubimov, A.Y. / Russi, S. / Cohen, A.E. / Narayanasamy, S.R. / Botha, S. / Kupitz, C. / Sierra, R.G. / Poitevin, F. / Gilardi, A. / Lisova, ...Authors: Liu, Z. / Gu, K.K. / Shelby, M.L. / Gilbile, D. / Lyubimov, A.Y. / Russi, S. / Cohen, A.E. / Narayanasamy, S.R. / Botha, S. / Kupitz, C. / Sierra, R.G. / Poitevin, F. / Gilardi, A. / Lisova, S. / Coleman, M.A. / Frank, M. / Kuhl, T.L.
History
DepositionApr 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.800, 78.800, 38.000
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

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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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 4.6 / Details: 2 M NaCl with 0.1 M sodium acetate buffer (pH 4.6)

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.25363 Å
DetectorType: SLAC ePix10k 2M / Detector: PIXEL / Date: Nov 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25363 Å / Relative weight: 1
ReflectionResolution: 1.7→24.82 Å / Num. obs: 13913 / % possible obs: 99.8 % / Redundancy: 809 % / Biso Wilson estimate: 15.83 Å2 / CC1/2: 0.948 / CC star: 0.9866 / Net I/σ(I): 4.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 435 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1353 / CC1/2: 0.4542 / CC star: 0.7903 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
CrystFEL0.9.1data collection
XDSJan 10, 2022data reduction
pointless1.12.2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→22.47 Å / SU ML: 0.3495 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5636
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2814 657 4.88 %
Rwork0.2512 12815 -
obs0.2527 13472 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.95 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 79 1080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071021
X-RAY DIFFRACTIONf_angle_d0.93561381
X-RAY DIFFRACTIONf_chiral_restr0.0569144
X-RAY DIFFRACTIONf_plane_restr0.0102181
X-RAY DIFFRACTIONf_dihedral_angle_d7.0018143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.60981330.59072455X-RAY DIFFRACTION96.57
1.83-2.020.31571170.30972477X-RAY DIFFRACTION96.75
2.02-2.310.28651310.23752572X-RAY DIFFRACTION100
2.31-2.910.22531250.22012609X-RAY DIFFRACTION100
2.91-22.470.27521510.23632702X-RAY DIFFRACTION99.03

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