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- PDB-5i4x: Exploring onset of lysozyme denaturation by urea - soak period 2 hours -

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Basic information

Entry
Database: PDB / ID: 5i4x
TitleExploring onset of lysozyme denaturation by urea - soak period 2 hours
ComponentsLysozyme C
KeywordsHYDROLASE / Lysozyme / urea / denaturation
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / 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 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)14,82210
Polymers14,3311
Non-polymers4919
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6500 Å2
Unit cell
Length a, b, c (Å)78.840, 78.840, 36.840
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-441-

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


Mass: 60.055 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH4N2O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 38.42 %
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: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.607→30.73 Å / Num. obs: 15398 / % possible obs: 98.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 16.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0365 / Net I/σ(I): 14.29

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 1.607→30.73 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.15
RfactorNum. reflection% reflection
Rfree0.2127 767 4.98 %
Rwork0.1776 --
obs0.1793 15398 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.607→30.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 30 145 1176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061055
X-RAY DIFFRACTIONf_angle_d1.0141416
X-RAY DIFFRACTIONf_dihedral_angle_d12.44369
X-RAY DIFFRACTIONf_chiral_restr0.042145
X-RAY DIFFRACTIONf_plane_restr0.004191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6073-1.73140.2491610.21412829X-RAY DIFFRACTION99
1.7314-1.90560.25151500.19032917X-RAY DIFFRACTION100
1.9056-2.18120.22541590.16112946X-RAY DIFFRACTION100
2.1812-2.74790.19271550.17862932X-RAY DIFFRACTION99
2.7479-30.74090.20211420.17423007X-RAY DIFFRACTION95

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