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- PDB-9hc2: Crystal structure of Lysozyme in complex with Gentisic Acid -

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Basic information

Entry
Database: PDB / ID: 9hc2
TitleCrystal structure of Lysozyme in complex with Gentisic Acid
ComponentsLysozyme C
KeywordsHYDROLASE / Globular / Enzyme
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
2,5-dihydroxybenzoic acid / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsIfeagwu, M.C. / Flood, R.J. / Mockler, N.M. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/RC/2275_P2 Ireland
CitationJournal: To Be Published
Title: Crystal structure of Lysozyme in complex with Gentisic Acid
Authors: Ifeagwu, M.C. / Flood, R.J. / Mockler, N.M. / Crowley, P.B.
History
DepositionNov 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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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)14,9508
Polymers14,3311
Non-polymers6197
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint8 kcal/mol
Surface area6650 Å2
Unit cell
Length a, b, c (Å)77.974, 77.974, 37.090
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-324-

HOH

21A-360-

HOH

31A-379-

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-GTQ / 2,5-dihydroxybenzoic acid


Mass: 154.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.95 Å3/Da / Density % sol: 36.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100 mM tri-Sodium citrate pH 4.0, 800 mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 7, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.27→55.14 Å / Num. obs: 30172 / % possible obs: 98.1 % / Redundancy: 21.8 % / CC1/2: 1 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.019 / Rrim(I) all: 0.091 / Net I/σ(I): 15.6
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 7.3 % / Rmerge(I) obs: 3.111 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1266 / CC1/2: 0.325 / Rpim(I) all: 1.193 / Rrim(I) all: 3.348 / % possible all: 84.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS1.20.1_4487data reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→55.14 Å / SU ML: 0.1584 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2263
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.209 1535 5.25 %
Rwork0.192 27695 -
obs0.1929 29230 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.32 Å2
Refinement stepCycle: LAST / Resolution: 1.27→55.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 42 80 1123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811058
X-RAY DIFFRACTIONf_angle_d0.9841421
X-RAY DIFFRACTIONf_chiral_restr0.0972144
X-RAY DIFFRACTIONf_plane_restr0.0095185
X-RAY DIFFRACTIONf_dihedral_angle_d12.7847372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.310.329680.34911435X-RAY DIFFRACTION55.14
1.31-1.360.32541500.30422323X-RAY DIFFRACTION89.93
1.36-1.410.27981250.26332608X-RAY DIFFRACTION99.17
1.41-1.480.25491720.22262587X-RAY DIFFRACTION100
1.48-1.550.2481290.20142630X-RAY DIFFRACTION100
1.55-1.650.20721500.18832607X-RAY DIFFRACTION100
1.65-1.780.22951370.19392650X-RAY DIFFRACTION100
1.78-1.960.19471330.19172674X-RAY DIFFRACTION100
1.96-2.240.23161440.18322649X-RAY DIFFRACTION99.93
2.24-2.820.20241660.18822692X-RAY DIFFRACTION100
2.82-55.140.18271610.1772840X-RAY DIFFRACTION99.9

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