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- PDB-5i4y: Exploring onset of lysozyme denaturation by urea: soak period 10 ... -

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Basic information

Entry
Database: PDB / ID: 5i4y
TitleExploring onset of lysozyme denaturation by urea: soak period 10 hours.
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / denaturation / urea
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.607 Å
AuthorsHosur, M.V. / Raskar, T. / Khavnekar, S.
CitationJournal: Sci Rep / Year: 2016
Title: Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation
Authors: Raskar, T. / Khavnekar, S. / Hosur, M.
History
DepositionFeb 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,62823
Polymers14,3311
Non-polymers1,29722
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint5 kcal/mol
Surface area6880 Å2
Unit cell
Length a, b, c (Å)78.650, 78.650, 36.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-201-

URE

21A-201-

URE

31A-202-

URE

41A-202-

URE

51A-376-

HOH

61A-383-

HOH

71A-434-

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-URE / UREA / Urea


Mass: 60.055 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: CH4N2O
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: sodium chloride, sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.607→33.33 Å / Num. obs: 15261 / % possible obs: 98.19 % / Redundancy: 1.8 % / Biso Wilson estimate: 16.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0505 / Net I/σ(I): 11.62

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193L

193l


Resolution: 1.607→33.33 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.64
RfactorNum. reflection% reflection
Rfree0.211 761 4.99 %
Rwork0.1816 --
obs0.183 15259 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.607→33.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 85 137 1223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071088
X-RAY DIFFRACTIONf_angle_d1.0341444
X-RAY DIFFRACTIONf_dihedral_angle_d11.745365
X-RAY DIFFRACTIONf_chiral_restr0.045144
X-RAY DIFFRACTIONf_plane_restr0.003202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6075-1.73160.311470.25732794X-RAY DIFFRACTION97
1.7316-1.90580.27891590.21622882X-RAY DIFFRACTION100
1.9058-2.18150.22031600.17632922X-RAY DIFFRACTION100
2.1815-2.74830.18551520.17472944X-RAY DIFFRACTION100
2.7483-33.3390.18731430.16652956X-RAY DIFFRACTION94

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