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- PDB-6b7v: Structure of hen egg-white lysozyme pre-treated with high-pressur... -

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Basic information

Entry
Database: PDB / ID: 6b7v
TitleStructure of hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa
ComponentsLysozyme C
KeywordsHYDROLASE / Lysozyme / pressure / pre-treated / homogenization method
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
Lysozyme - #10 / 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 / Lysozyme-like domain superfamily ...Lysozyme - #10 / 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 / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.482 Å
AuthorsMorais, M.A.B. / Nascimento, A.F.Z. / Tominaga, C.Y. / Cristianini, M. / Tribst, A.A.L. / Murakami, M.T.
CitationJournal: Innov Food Sci Emerg Technol / Year: 2018
Title: How high pressure pre-treatments affect the function and structure of hen egg-white lysozyme
Authors: Morais, M.A.B. / Nascimento, A.F.Z. / Tominaga, C.Y. / Cristianini, M. / Tribst, A.A.L. / Murakami, M.T.
History
DepositionOct 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,92813
Polymers14,3311
Non-polymers59712
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-73 kcal/mol
Surface area6470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.144, 78.144, 36.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-326-

HOH

21A-348-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 128 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.7M sodium chloride, 0.1M sodium acetate pH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.48→34.95 Å / Num. obs: 19194 / % possible obs: 97.98 % / Redundancy: 22 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.04681 / Rrim(I) all: 0.04789 / Net I/σ(I): 41.89
Reflection shell
Lowest resolution (Å)Diffraction-ID
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33.441

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
SHELXphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.482→33.44 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.94
RfactorNum. reflection% reflection
Rfree0.2033 960 5 %
Rwork0.1676 --
obs0.1694 19188 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 50.68 Å2 / Biso mean: 19.65 Å2 / Biso min: 9.46 Å2
Refinement stepCycle: final / Resolution: 1.482→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 31 116 1147
Biso mean--35.73 28.62 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061043
X-RAY DIFFRACTIONf_angle_d1.0141398
X-RAY DIFFRACTIONf_chiral_restr0.044144
X-RAY DIFFRACTIONf_plane_restr0.004183
X-RAY DIFFRACTIONf_dihedral_angle_d11.404368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4819-1.56010.20321230.19822336245990
1.5601-1.65780.19971330.17562535266897
1.6578-1.78580.21811360.17362579271599
1.7858-1.96550.2241390.162826312770100
1.9655-2.24990.18641380.161626342772100
2.2499-2.83440.2261420.17626992841100
2.8344-33.44860.191490.16228142963100

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