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- PDB-9i6m: Hen egg-white lysozyme structure at 65% relative humidity -

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Basic information

Entry
Database: PDB / ID: 9i6m
TitleHen egg-white lysozyme structure at 65% relative humidity
ComponentsLysozyme C
KeywordsHYDROLASE
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: 1.7 Å
AuthorsZabelskii, D. / Round, E. / Han, H. / von Stetten, D. / Melo, D. / de Wijn, R. / Bean, R. / Round, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Viscoelastic characterization of the lipid cubic phase provides insights into high-viscosity extrusion injection for XFEL experiments.
Authors: Zabelskii, D. / Round, E. / Han, H. / von Stetten, D. / Letrun, R. / Kim, C. / Sato, T. / Melo, D. / de Wijn, R. / Kharitonov, K. / Smyth, P. / Doerner, K. / Kloos, M. / Dietze, T. / Lopez, ...Authors: Zabelskii, D. / Round, E. / Han, H. / von Stetten, D. / Letrun, R. / Kim, C. / Sato, T. / Melo, D. / de Wijn, R. / Kharitonov, K. / Smyth, P. / Doerner, K. / Kloos, M. / Dietze, T. / Lopez, L. / Bean, R. / Round, A.
History
DepositionJan 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: 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)14,78011
Polymers14,3311
Non-polymers44910
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-41 kcal/mol
Surface area6560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.000, 79.000, 38.000
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-1139-

HOH

21A-1194-

HOH

31A-1221-

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-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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 297 K / Method: small tubes / pH: 3 / Details: 20% NaCl, 6% PEG 6000, 0.1M sodium acetate pH 3.0 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 297 K / Ambient temp details: Room temperature / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→55.86 Å / Num. obs: 13878 / % possible obs: 99.7 % / Redundancy: 234.4 % / Biso Wilson estimate: 20.32 Å2 / CC1/2: 0.983 / CC star: 0.9957 / R split: 0.1105 / Net I/σ(I): 7.62
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 138.1 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1341 / CC1/2: 0.6977 / CC star: 0.9066 / R split: 0.4212 / % possible all: 99.8
Serial crystallography measurementPulse energy: 12700 µJ
Serial crystallography sample deliveryDescription: fixed target / Method: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFEL0.10.1data reduction
CrystFEL0.10.1data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→55.86 Å / SU ML: 0.1965 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.8268
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1987 652 4.74 %
Rwork0.1612 13102 -
obs0.163 13754 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.47 Å2
Refinement stepCycle: LAST / Resolution: 1.7→55.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 22 121 1144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01631122
X-RAY DIFFRACTIONf_angle_d1.52111520
X-RAY DIFFRACTIONf_chiral_restr0.0938155
X-RAY DIFFRACTIONf_plane_restr0.0173203
X-RAY DIFFRACTIONf_dihedral_angle_d12.6684422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.23451200.22672577X-RAY DIFFRACTION99.89
1.83-2.020.1921310.15132558X-RAY DIFFRACTION100
2.02-2.310.21311190.15942593X-RAY DIFFRACTION100
2.31-2.910.19351490.17182606X-RAY DIFFRACTION100
2.91-55.860.19291330.152768X-RAY DIFFRACTION100

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