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- PDB-9hru: The Lysozyme - pctx complex in space group P3121 -

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Basic information

Entry
Database: PDB / ID: 9hru
TitleThe Lysozyme - pctx complex in space group P3121
ComponentsLysozyme C
KeywordsHYDROLASE / Complex
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: 1.88 Å
AuthorsWren, C.P. / Flood, R.J. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/RC/2275_P2 Ireland
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Protein Recognition and Assembly by a Phosphocavitand.
Authors: Wren, C.P. / Flood, R.J. / Mockler, N.M. / Savko, M. / Malinska, M. / Shi, Q. / Crowley, P.B.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,70711
Polymers28,6622
Non-polymers2,0449
Water1,910106
1
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4516
Polymers14,3311
Non-polymers1,1205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2565
Polymers14,3311
Non-polymers9254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.307, 86.307, 72.738
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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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.: 2 / Mutation: 0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-A1IXG / phosphated-cyclotrixylohydroquinoylene


Mass: 636.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H27O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.56 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M magnesium sulfate, 0.1 M MES pH 6.5

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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: Nov 11, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.88→52.13 Å / Num. obs: 25883 / % possible obs: 100 % / Redundancy: 17.3 % / Biso Wilson estimate: 31.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.027 / Rrim(I) all: 0.111 / Net I/σ(I): 16.6
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 18.2 % / Rmerge(I) obs: 1.55 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1268 / CC1/2: 0.849 / Rpim(I) all: 0.374 / Rrim(I) all: 1.595 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→52.13 Å / SU ML: 0.2132 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.9436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2241 1323 5.12 %
Rwork0.1913 24529 -
obs0.193 25852 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.6 Å2
Refinement stepCycle: LAST / Resolution: 1.88→52.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 126 106 2234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822173
X-RAY DIFFRACTIONf_angle_d1.11352976
X-RAY DIFFRACTIONf_chiral_restr0.0552289
X-RAY DIFFRACTIONf_plane_restr0.0086434
X-RAY DIFFRACTIONf_dihedral_angle_d14.4969814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.950.32451190.2532686X-RAY DIFFRACTION99.79
1.95-2.040.29311350.22092708X-RAY DIFFRACTION99.93
2.04-2.150.22671710.19832679X-RAY DIFFRACTION99.69
2.15-2.290.25911430.19072690X-RAY DIFFRACTION99.86
2.29-2.460.25161390.1882711X-RAY DIFFRACTION99.89
2.46-2.710.22331540.21322709X-RAY DIFFRACTION99.97
2.71-3.10.24871660.21322704X-RAY DIFFRACTION99.83
3.1-3.910.22551390.18032780X-RAY DIFFRACTION99.86
3.91-52.130.18981570.17592862X-RAY DIFFRACTION99.9

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