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- PDB-5kj9: Anticancer activity of Ru- and Os(arene) compounds of a maleimide... -

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Basic information

Entry
Database: PDB / ID: 5kj9
TitleAnticancer activity of Ru- and Os(arene) compounds of a maleimide-functionalized bioactive pyridinecarbothioamide ligand
ComponentsLysozyme C
KeywordsHYDROLASE / Lysozyme / Anticancer / Ligand / Ruthenium
Function / homology
Function and homology information


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 Gram-positive bacterium / defense response to bacterium ...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 Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / 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 / Lysozyme-like domain superfamily ...Lysozyme - #10 / 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 / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RUTHENIUM ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsSullivan, M.P. / Christian, C.G. / Goldstone, D.C.
CitationJournal: J. Inorg. Biochem. / Year: 2016
Title: Anticancer activity of Ru- and Os(arene) compounds of a maleimide-functionalized bioactive pyridinecarbothioamide ligand.
Authors: Hanif, M. / Moon, S. / Sullivan, M.P. / Movassaghi, S. / Kubanik, M. / Goldstone, D.C. / Sohnel, T. / Jamieson, S.M. / Hartinger, C.G.
History
DepositionJun 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4553
Polymers14,3311
Non-polymers1242
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area6570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.580, 78.580, 37.480
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-329-

HOH

21A-358-

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-RU / RUTHENIUM ION / Ruthenium


Mass: 101.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ru
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100mg/mL hen egg white lysozyme, 0.8 M NaCl, 0.1 M sodium acetate pH 4.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.2→55.565 Å / Num. obs: 37155 / % possible obs: 99.7 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.02 / Rrim(I) all: 0.059 / Net I/σ(I): 19 / Num. measured all: 335832 / Scaling rejects: 322
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.2-1.2290.5221646618230.9110.1830.5553.7100
6.57-21.795.80.04212272110.9950.0180.04636.677.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.39 Å21.47 Å
Translation5.39 Å21.47 Å

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Processing

Software
NameVersionClassification
MOSFLM7.2.1data reduction
Aimless0.5.23data scaling
PHASER2.6.1phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NHI

4nhi


Resolution: 1.2→55.56 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.206 / SU ML: 0.025 / SU R Cruickshank DPI: 0.0432 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.043
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 1801 4.9 %RANDOM
Rwork0.1665 ---
obs0.168 35303 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 41.51 Å2 / Biso mean: 15.464 Å2 / Biso min: 7.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 1.2→55.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 2 93 1096
Biso mean--18.79 23.44 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191068
X-RAY DIFFRACTIONr_bond_other_d0.0020.02993
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9051458
X-RAY DIFFRACTIONr_angle_other_deg1.00832267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0185141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88422.64253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55615178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9231513
X-RAY DIFFRACTIONr_chiral_restr0.0910.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021271
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02288
X-RAY DIFFRACTIONr_mcbond_it1.0821.339529
X-RAY DIFFRACTIONr_mcbond_other1.0791.335528
X-RAY DIFFRACTIONr_mcangle_it1.5272.019663
X-RAY DIFFRACTIONr_rigid_bond_restr1.08732060
X-RAY DIFFRACTIONr_sphericity_free21.95533
X-RAY DIFFRACTIONr_sphericity_bonded7.81952092
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 136 -
Rwork0.186 2579 -
all-2715 -
obs--100 %

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