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- PDB-8rge: Serial synchrotron in plate room temperature structure of Lysozyme. -

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Basic information

Entry
Database: PDB / ID: 8rge
TitleSerial synchrotron in plate room temperature structure of Lysozyme.
ComponentsLysozyme C
KeywordsHYDROLASE / Lysozyme 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsThompson, A.J. / Hough, M.A. / Sanchez-Weatherby, J. / Williams, L.J. / Sandy, J. / Worrall, J.A.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Efficient in situ screening of and data collection from microcrystals in crystallization plates.
Authors: Thompson, A.J. / Sanchez-Weatherby, J. / Williams, L.J. / Mikolajek, H. / Sandy, J. / Worrall, J.A.R. / Hough, M.A.
History
DepositionDec 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)14,3903
Polymers14,3311
Non-polymers582
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-20 kcal/mol
Surface area6610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.573, 78.573, 37.768
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-360-

HOH

21A-364-

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 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 3.5 / Details: 1M acetic acid pH 3, 5 % Peg 6000, 20 % NaCl

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: Room temperature / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.775 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: May 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.775 Å / Relative weight: 1
ReflectionResolution: 1.88→55.56 Å / Num. obs: 10076 / % possible obs: 99.27 % / Redundancy: 110.9 % / Biso Wilson estimate: 31.36 Å2 / CC1/2: 0.997 / R split: 0.083 / Net I/σ(I): 19.1
Reflection shellResolution: 1.88→1.947 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 973 / CC1/2: 0.398 / R split: 1.143
Serial crystallography sample deliveryDescription: In Plate / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Mitegen in situ-1 plate

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→55.56 Å / SU ML: 0.2563 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.38
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2306 510 5.1 %
Rwork0.1926 9492 -
obs0.1947 10002 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.64 Å2
Refinement stepCycle: LAST / Resolution: 1.88→55.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 2 83 1086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721110
X-RAY DIFFRACTIONf_angle_d0.90281514
X-RAY DIFFRACTIONf_chiral_restr0.0555155
X-RAY DIFFRACTIONf_plane_restr0.0201204
X-RAY DIFFRACTIONf_dihedral_angle_d15.5014419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-2.070.33961310.25592319X-RAY DIFFRACTION99.92
2.07-2.370.34881170.25852307X-RAY DIFFRACTION97.86
2.37-2.980.28251200.21082377X-RAY DIFFRACTION100
2.98-55.560.1831420.16222489X-RAY DIFFRACTION99.32

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