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

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Basic information

Entry
Database: PDB / ID: 29lj
TitleX-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(D-p-CNPhF)(O2CCH3)3]
ComponentsLysozyme C
KeywordsMETAL BINDING PROTEIN / ruthenium / protein interactions action / 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 / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 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 19, 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)15,8649
Polymers14,3311
Non-polymers1,5338
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-8 kcal/mol
Surface area7470 Å2
Unit cell
Length a, b, c (Å)78.180, 78.180, 37.530
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-334-

HOH

21A-376-

HOH

31A-407-

HOH

41A-425-

HOH

51A-427-

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, 135 molecules

#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-A1IHW / 4-[11-(4-cyanophenyl)-1,5-bis($l^{3}-oxidanyl)-3,7-dimethyl-2$l^{3},4,6,8$l^{3}-tetraoxa-9$l^{4},11-diaza-1$l^{5},5$l^{5}-diruthenatricyclo[3.3.3.0^{1,5}]undeca-2,7,9-trien-9-yl]benzenecarbonitrile


Mass: 601.517 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19N4O6Ru2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.01 Å3/Da / Density % sol: 38.77 %
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: Jul 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→55.28 Å / Num. obs: 38424 / % possible obs: 86.94 % / Redundancy: 9.9 % / CC1/2: 1 / Rmerge(I) obs: 0.042 / Net I/σ(I): 21.8
Reflection shellResolution: 1.13→1.15 Å / Rmerge(I) obs: 0.836 / Num. unique obs: 36587 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→55.28 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.834 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2095 1837 4.781 %RANDOM
Rwork0.1982 36587 --
all0.199 ---
obs-38424 86.94 %-
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: 20.479 Å2
Baniso -1Baniso -2Baniso -3
1--0.078 Å2-0 Å20 Å2
2---0.078 Å2-0 Å2
3---0.156 Å2
Refinement stepCycle: LAST / Resolution: 1.13→55.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 81 127 1209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121168
X-RAY DIFFRACTIONr_bond_other_d0.0010.016999
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.8711600
X-RAY DIFFRACTIONr_angle_other_deg0.691.8082280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2785138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.297514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24310182
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.941055
X-RAY DIFFRACTIONr_chiral_restr0.110.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021527
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02307
X-RAY DIFFRACTIONr_nbd_refined0.250.2267
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.2919
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2540
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2554
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.283
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.230
X-RAY DIFFRACTIONr_nbd_other0.1920.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.228
X-RAY DIFFRACTIONr_mcbond_it1.9691.943541
X-RAY DIFFRACTIONr_mcbond_other1.9451.939540
X-RAY DIFFRACTIONr_mcangle_it2.8463.49682
X-RAY DIFFRACTIONr_mcangle_other2.8443.499683
X-RAY DIFFRACTIONr_scbond_it2.9862.337627
X-RAY DIFFRACTIONr_scbond_other3.0862.325560
X-RAY DIFFRACTIONr_scangle_it4.54.211918
X-RAY DIFFRACTIONr_scangle_other4.6734.098809
X-RAY DIFFRACTIONr_lrange_it7.78326.2661460
X-RAY DIFFRACTIONr_lrange_other7.52123.8011342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.1580.38790.36799X-RAY DIFFRACTION3.3697
1.158-1.190.309520.3211311X-RAY DIFFRACTION43.38
1.19-1.2250.369980.3332319X-RAY DIFFRACTION79.4021
1.225-1.2620.3941430.3182609X-RAY DIFFRACTION92.7224
1.262-1.3040.3241550.2982717X-RAY DIFFRACTION99.5839
1.304-1.3490.2731280.2862670X-RAY DIFFRACTION100
1.349-1.40.2521230.2632559X-RAY DIFFRACTION99.9627
1.4-1.4570.2761270.2492461X-RAY DIFFRACTION100
1.457-1.5220.2131250.2242375X-RAY DIFFRACTION100
1.522-1.5960.2321300.2212259X-RAY DIFFRACTION100
1.596-1.6830.2441090.2052160X-RAY DIFFRACTION100
1.683-1.7850.236910.22088X-RAY DIFFRACTION99.5887
1.785-1.9080.219860.1891940X-RAY DIFFRACTION99.7538
1.908-2.060.19840.1821816X-RAY DIFFRACTION99.7375
2.06-2.2570.217870.1731667X-RAY DIFFRACTION99.7725
2.257-2.5220.194760.1671537X-RAY DIFFRACTION99.6294
2.522-2.9120.201740.1631361X-RAY DIFFRACTION99.8608
2.912-3.5640.165650.1731147X-RAY DIFFRACTION99.6711
3.564-5.0290.167430.159932X-RAY DIFFRACTION99.8975
5.029-55.280.246320.325560X-RAY DIFFRACTION99.3289

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