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- PDB-7wxs: Lysozyme protected by polyacrylamide gel -

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Basic information

Entry
Database: PDB / ID: 7wxs
TitleLysozyme protected by polyacrylamide gel
ComponentsLysozyme C
KeywordsHYDROLASE / Hydrogel / polyacrylamide gel
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: 1.25 Å
AuthorsMuroyama, H. / Tomoike, F. / Nagae, T. / Okada, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K15713 Japan
CitationJournal: To Be Published
Title: Post-crystallization protection of protein crystals by polyacrylamide
Authors: Muroyama, H. / Kato, S. / Itabashi, T. / Nagae, T. / Okada, T. / Tomoike, F.
History
DepositionFeb 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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 C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4824
Polymers14,3311
Non-polymers1513
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area6600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.114, 79.114, 37.058
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-316-

HOH

21A-359-

HOH

31A-466-

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 / Details: NA / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 50mM sodium acetate, 1.5M NaCl, pH 4.5

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.25→25.02 Å / Num. obs: 32552 / % possible obs: 98.3 % / Redundancy: 6 % / Biso Wilson estimate: 9.53 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.13 / Net I/σ(I): 23.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.25-1.2960.5713.631120.7990.62398.3
1.29-1.354.40.4854.431590.860.5396.8
1.35-1.4160.3825.731700.90.41797.1
1.41-1.4860.3037.731970.9310.3397.2
1.48-1.5760.2410.731980.9540.26398.6
1.57-1.760.18615.532450.970.20398.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6lt5

6lt5


Resolution: 1.25→25.02 Å / SU ML: 0.0901 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.3568
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1948 1779 5.47 %
Rwork0.1778 30772 -
obs0.1788 32551 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.87 Å2
Refinement stepCycle: LAST / Resolution: 1.25→25.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 0 173 1182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481035
X-RAY DIFFRACTIONf_angle_d0.76631399
X-RAY DIFFRACTIONf_chiral_restr0.0811145
X-RAY DIFFRACTIONf_plane_restr0.0045183
X-RAY DIFFRACTIONf_dihedral_angle_d21.6018148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.24341310.22232275X-RAY DIFFRACTION96.32
1.28-1.320.26261330.2092286X-RAY DIFFRACTION96.34
1.32-1.360.23341320.1982292X-RAY DIFFRACTION96.96
1.36-1.410.21631340.19532313X-RAY DIFFRACTION97.45
1.41-1.470.21081330.17812304X-RAY DIFFRACTION97.64
1.47-1.540.19651340.17042330X-RAY DIFFRACTION97.93
1.54-1.620.16941370.16882354X-RAY DIFFRACTION98.07
1.62-1.720.17681360.16542361X-RAY DIFFRACTION99.05
1.72-1.850.19511370.17292371X-RAY DIFFRACTION98.9
1.85-2.040.18631400.16842411X-RAY DIFFRACTION99.53
2.04-2.330.1871380.17112411X-RAY DIFFRACTION99.61
2.33-2.940.18661440.18482463X-RAY DIFFRACTION100
2.94-25.020.19251500.17442601X-RAY DIFFRACTION99.96

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