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- PDB-29nx: X-ray structure of the adduct formed upon reaction of Lysozyme wi... -

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Basic information

Entry
Database: PDB / ID: 29nx
TitleX-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(D-p-TolF)(O2CCH3)3]
ComponentsLysozyme C
KeywordsMETAL BINDING PROTEIN / ruthenium / diruthenium / protein interaction / metallodrug
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 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 bacterium / defense response to Gram-positive bacterium / Golgi apparatus / endoplasmic reticulum / : / 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
: / NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTeran, A. / Ferraro, G. / Merlino, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Inorg.Chem. / Year: 2026
Title: Protein Recognition and Amyloid Remodeling Governed by Paddlewheel Diruthenium Coordination Chemistry.
Authors: La Manna, S. / Florio, D. / Ferraro, G. / Policino, M.R. / Altieri, F. / Teran, A. / Herrero, S. / Merlino, A. / Marasco, D.
History
DepositionMar 25, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)16,51611
Polymers14,3311
Non-polymers2,18510
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.530, 77.530, 37.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-342-

HOH

21A-392-

HOH

31A-395-

HOH

41A-401-

HOH

51A-402-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 113 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-A1J4C / 3,7-dimethyl-9,11-bis(4-methylphenyl)-1,5-bis(oxidanyl)-2,4,6,8-tetraoxa-9,11-diaza-1$l^{5},5$l^{5}-diruthenatricyclo[3.3.3.0^{1,5}]undecane


Mass: 605.589 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N2O6Ru2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.97 Å3/Da / Density % sol: 37.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% ethylene glycol, 0.1 M sodium acetate at pH 4.0, and 0.6 M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→54.822 Å / Num. obs: 28706 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 1 / Net I/σ(I): 31.5
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 1400 / CC1/2: 0.775

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→54.822 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.118 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 1364 4.752 %RANDOM
Rwork0.1991 27342 --
all0.2 ---
obs-28706 99.889 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.865 Å2
Baniso -1Baniso -2Baniso -3
1--0.014 Å2-0 Å20 Å2
2---0.014 Å2-0 Å2
3---0.028 Å2
Refinement stepCycle: LAST / Resolution: 1.3→54.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 109 103 1213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0111196
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161001
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9071652
X-RAY DIFFRACTIONr_angle_other_deg0.6721.8072282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3625136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.806514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61610182
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.8641055
X-RAY DIFFRACTIONr_chiral_restr0.1070.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021572
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02307
X-RAY DIFFRACTIONr_nbd_refined0.2590.2268
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.2933
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2538
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2532
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.273
X-RAY DIFFRACTIONr_metal_ion_refined0.1020.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.219
X-RAY DIFFRACTIONr_nbd_other0.210.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.220
X-RAY DIFFRACTIONr_mcbond_it2.1212.149535
X-RAY DIFFRACTIONr_mcbond_other2.1092.147535
X-RAY DIFFRACTIONr_mcangle_it3.0243.866674
X-RAY DIFFRACTIONr_mcangle_other3.033.871675
X-RAY DIFFRACTIONr_scbond_it3.2942.627661
X-RAY DIFFRACTIONr_scbond_other3.1862.546547
X-RAY DIFFRACTIONr_scangle_it4.9664.747978
X-RAY DIFFRACTIONr_scangle_other4.9754.494796
X-RAY DIFFRACTIONr_lrange_it6.84326.4111476
X-RAY DIFFRACTIONr_lrange_other6.722.8591306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.3-1.3340.277900.29920060.29820960.950.9461000.277
1.334-1.370.305920.29719300.29720250.9460.94599.85190.267
1.37-1.410.3061030.27618840.27819880.9360.95199.94970.236
1.41-1.4530.274940.26718080.26819020.9540.9551000.228
1.453-1.5010.247950.24617800.24618750.960.9621000.205
1.501-1.5540.226820.22917080.22817910.9630.96699.94420.189
1.554-1.6120.263850.21816870.2217720.960.9691000.181
1.612-1.6780.221920.20415810.20516730.9690.9731000.173
1.678-1.7530.337740.21615490.22116230.9280.9691000.185
1.753-1.8380.272920.20614570.2115490.9580.9721000.187
1.838-1.9370.208670.20814140.20814830.9650.97399.86510.191
1.937-2.0550.242550.19613480.19814030.9590.9751000.189
2.055-2.1960.207480.18312860.18413350.9740.97999.92510.189
2.196-2.3720.188610.16811800.16912410.980.9821000.177
2.372-2.5980.221590.16510790.16811390.9660.98199.91220.182
2.598-2.9040.22560.17310150.17510710.9730.9791000.2
2.904-3.3510.177410.1738790.1739210.9770.98199.89140.21
3.351-4.1010.184350.1657620.1668060.9790.98398.88340.21
4.101-5.7830.242310.196090.1936430.9720.97999.53340.255
5.783-54.8220.331120.3363740.3363960.9550.92397.47470.428

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