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

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Basic information

Entry
Database: PDB / ID: 29mn
TitleX-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(p-TolA)(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
ACETATE ION / NITRATE ION / RUTHENIUM ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.311 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 23, 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)15,22514
Polymers14,3311
Non-polymers89413
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-11 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.120, 78.120, 37.580
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-335-

HOH

21A-360-

HOH

31A-372-

HOH

41A-438-

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 , 6 types, 152 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.: 6 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ru / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2 Å3/Da / Density % sol: 38.51 %
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: 1.31→55.24 Å / Num. obs: 30924 / % possible obs: 99.6 % / Redundancy: 12.9 % / CC1/2: 1 / Net I/σ(I): 27
Reflection shellResolution: 1.31→1.33 Å / Num. unique obs: 1403 / CC1/2: 0.806

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.311→55.239 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.028 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1382 4.872 %RANDOM
Rwork0.183 26987 --
all0.184 ---
obs-26987 99.6 %-
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: 21.819 Å2
Baniso -1Baniso -2Baniso -3
1--0.493 Å2-0 Å20 Å2
2---0.493 Å2-0 Å2
3---0.985 Å2
Refinement stepCycle: LAST / Resolution: 1.311→55.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 46 127 1174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161055
X-RAY DIFFRACTIONr_angle_refined_deg1.9851.7951631
X-RAY DIFFRACTIONr_angle_other_deg0.6941.8142417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.146514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42710194
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.9681060
X-RAY DIFFRACTIONr_chiral_restr0.1090.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021607
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02329
X-RAY DIFFRACTIONr_nbd_refined0.2470.2272
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.2946
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2561
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2567
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.283
X-RAY DIFFRACTIONr_metal_ion_refined0.060.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2640.219
X-RAY DIFFRACTIONr_nbd_other0.1880.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2430.232
X-RAY DIFFRACTIONr_mcbond_it1.9712.11581
X-RAY DIFFRACTIONr_mcbond_other1.932.105580
X-RAY DIFFRACTIONr_mcangle_it2.8563.796746
X-RAY DIFFRACTIONr_mcangle_other2.8713.804747
X-RAY DIFFRACTIONr_scbond_it3.3592.534611
X-RAY DIFFRACTIONr_scbond_other3.3042.518598
X-RAY DIFFRACTIONr_scangle_it5.0214.507885
X-RAY DIFFRACTIONr_scangle_other4.9994.428862
X-RAY DIFFRACTIONr_lrange_it6.67826.211445
X-RAY DIFFRACTIONr_lrange_other6.57924.6021407
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
1.311-1.3450.3181030.28519480.28620660.9320.94499.2740.266
1.345-1.3820.3171140.2818870.28220010.9320.9461000.252
1.382-1.4220.308840.25918790.26119790.9520.95699.19150.226
1.422-1.4660.238880.24817960.24718940.9630.9699.4720.213
1.466-1.5140.21800.22517620.22418490.9720.96799.62140.185
1.514-1.5670.274840.22317110.22518000.9480.96999.72220.183
1.567-1.6260.229830.19916460.217350.970.97499.65420.162
1.626-1.6920.272880.20415630.20716610.9490.97499.39790.166
1.692-1.7670.208790.19915290.19916160.9780.97699.50490.166
1.767-1.8540.224780.19914530.215350.9720.97599.73940.171
1.854-1.9540.186730.18613880.18614660.9750.97999.65890.168
1.954-2.0720.202710.1813180.18113950.9710.9899.56990.17
2.072-2.2150.18560.1812630.1813230.9810.98199.69770.179
2.215-2.3920.225640.15811560.16212230.9730.98599.75470.166
2.392-2.620.178680.15710590.15911300.9820.98499.73450.171
2.62-2.9280.157360.15210110.15210510.9820.98599.61940.173
2.928-3.380.186450.1688760.1689220.9790.98299.89150.201
3.38-4.1350.148420.1467610.1478040.9860.98799.87560.184
4.135-5.8320.178230.1816070.1816320.9810.98499.68350.24
5.832-55.2390.176220.2733650.2683910.9680.94798.9770.327

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