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- PDB-6lt5: Lysozyme protected by alginate gel -

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Basic information

Entry
Database: PDB / ID: 6lt5
TitleLysozyme protected by alginate gel
ComponentsLysozyme C
KeywordsHYDROLASE / Hydrogel Alginate 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: 1.32 Å
AuthorsTomoike, F. / Morita, S. / Nagae, T. / Okada, T.
CitationJournal: To Be Published
Title: Post-crystallization protection of protein crystals
Authors: Morita, S. / Itabashi, T. / Nagae, T. / Takeuchi, S. / Okada, T. / Tomoike, F.
History
DepositionJan 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Data collection / Database references
Category: database_2 / diffrn_radiation_wavelength / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 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)14,80810
Polymers14,3311
Non-polymers4779
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-24 kcal/mol
Surface area6570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.097, 79.097, 36.962
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-342-

HOH

21A-385-

HOH

31A-438-

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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: 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.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 39.02 %
Crystal growTemperature: 277 K / Method: counter-diffusion / 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: Dec 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.3→35.37 Å / Num. obs: 29447 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 11.47 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.5
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 2 / Num. unique obs: 1401 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dpx

1dpx


Resolution: 1.32→30.84 Å / SU ML: 0.1206 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.5263
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1796 1442 5.13 %
Rwork0.1699 26657 -
obs0.1704 28099 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.83 Å2
Refinement stepCycle: LAST / Resolution: 1.32→30.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 24 142 1167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531045
X-RAY DIFFRACTIONf_angle_d0.78031409
X-RAY DIFFRACTIONf_chiral_restr0.0804145
X-RAY DIFFRACTIONf_plane_restr0.0045183
X-RAY DIFFRACTIONf_dihedral_angle_d17.9133378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.370.26381490.23292606X-RAY DIFFRACTION99.86
1.37-1.420.24951500.20672600X-RAY DIFFRACTION99.96
1.42-1.490.20011320.17612619X-RAY DIFFRACTION99.82
1.49-1.570.18131610.17052597X-RAY DIFFRACTION99.89
1.57-1.660.18471210.15862666X-RAY DIFFRACTION100
1.66-1.790.19611550.16532630X-RAY DIFFRACTION99.96
1.79-1.970.18931290.16152689X-RAY DIFFRACTION100
1.97-2.260.16721490.15432671X-RAY DIFFRACTION100
2.26-2.840.16831260.17362743X-RAY DIFFRACTION100
2.84-30.840.16391700.16852836X-RAY DIFFRACTION99.9

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