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

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Basic information

Entry
Database: PDB / ID: 29my
TitleX-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(D-o-TolF)(O2CCH3)3]
ComponentsLysozyme C
KeywordsMETAL BINDING PROTEIN / ruthenium / protein interaction / metallodrug / diruthenium
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: 1.747 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 24, 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)15,6898
Polymers14,3311
Non-polymers1,3587
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.690, 77.690, 37.510
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-320-

HOH

21A-350-

HOH

31A-362-

HOH

41A-364-

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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-A1J46 / 3,7-dimethyl-9,11-bis(2-methylphenyl)-2,4,6,8-tetraoxa-9,11-diaza-1$l^{4},5$l^{4}-diruthenatricyclo[3.3.3.0^{1,5}]undecane


Mass: 543.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21N2O4Ru2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 1.97 Å3/Da / Density % sol: 37.71 %
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: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.747→38.88 Å / Num. obs: 12107 / % possible obs: 99.4 % / Redundancy: 21.8 % / CC1/2: 0.993 / Net I/σ(I): 9.7
Reflection shellResolution: 1.747→1.77 Å / Num. unique obs: 614 / CC1/2: 0.805

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.747→38.843 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.768 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.146
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 586 4.852 %RANDOM
Rwork0.2221 11491 --
all0.224 ---
obs-11491 99.416 %-
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: 34.078 Å2
Baniso -1Baniso -2Baniso -3
1--0.328 Å2-0 Å20 Å2
2---0.328 Å2-0 Å2
3---0.655 Å2
Refinement stepCycle: LAST / Resolution: 1.747→38.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 69 64 1134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121172
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161003
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.8431608
X-RAY DIFFRACTIONr_angle_other_deg0.6081.8062296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8395142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.911511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32610183
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.6691057
X-RAY DIFFRACTIONr_chiral_restr0.0880.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021546
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02304
X-RAY DIFFRACTIONr_nbd_refined0.2450.2266
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.2943
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2539
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2546
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.250
X-RAY DIFFRACTIONr_metal_ion_refined0.1720.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.217
X-RAY DIFFRACTIONr_nbd_other0.1360.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.217
X-RAY DIFFRACTIONr_mcbond_it2.9273.247550
X-RAY DIFFRACTIONr_mcbond_other2.9173.244550
X-RAY DIFFRACTIONr_mcangle_it3.9255.843698
X-RAY DIFFRACTIONr_mcangle_other3.9435.85699
X-RAY DIFFRACTIONr_scbond_it4.0233.975622
X-RAY DIFFRACTIONr_scbond_other3.6883.697552
X-RAY DIFFRACTIONr_scangle_it5.9077.239910
X-RAY DIFFRACTIONr_scangle_other5.6446.615806
X-RAY DIFFRACTIONr_lrange_it8.20840.4151422
X-RAY DIFFRACTIONr_lrange_other8.28135.9041322
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
1.747-1.7920.433460.3698250.3728860.8490.8998.3070.36
1.792-1.8410.272380.2658050.2658470.9510.94399.52770.249
1.841-1.8950.326440.2537930.2578410.9360.95299.52440.234
1.895-1.9530.269490.2247500.2267990.9510.9641000.208
1.953-2.0170.315450.257110.2547810.9360.9696.7990.23
2.017-2.0870.291340.2497220.2517660.9420.95898.69450.237
2.087-2.1660.298290.2197040.2237330.9390.9661000.209
2.166-2.2540.307340.2216750.2257100.9410.96699.85920.213
2.254-2.3540.273360.2036530.2076900.9510.97299.85510.202
2.354-2.4680.248330.2076080.216410.9470.9721000.205
2.468-2.6010.205250.2025930.2026220.9740.97299.35690.208
2.601-2.7580.291230.2085750.2125980.9630.971000.216
2.758-2.9470.202230.1915310.1915560.9730.97499.64030.203
2.947-3.1820.225230.2035130.2045370.9640.97199.81380.213
3.182-3.4830.293190.2174640.2194830.9590.9731000.23
3.483-3.8910.221250.1994220.24470.9670.9791000.226
3.891-4.4850.214190.1943790.1953980.9660.971000.226
4.485-5.4750.272180.2113320.2143500.9420.971000.257
5.475-7.6670.249190.2472590.2472780.9590.961000.321
7.667-38.8430.11540.3561730.351800.9910.91198.33330.497

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