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- PDB-6wgo: The interaction of dichlorido(3-(anthracen-9-ylmethyl)-1-methylim... -

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Basic information

Entry
Database: PDB / ID: 6wgo
TitleThe interaction of dichlorido(3-(anthracen-9-ylmethyl)-1-methylimidazol-2-ylidene)(eta6-p-cymene)ruthenium(II) with HEWL after 1 week
ComponentsLysozyme
KeywordsHYDROLASE / metal-based / anticancer / ruthenium / NHC / carbene / HEWL / Hen egg White Lysozyme / lysozyme / metallodrug / imidazole / dimethylimidazole
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
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 / Chem-U0J / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsSullivan, M.P. / Hartinger, C.G. / Goldstone, D.C.
CitationJournal: Inorg.Chem. / Year: 2021
Title: Anthracenyl Functionalization of Half-Sandwich Carbene Complexes: In Vitro Anticancer Activity and Reactions with Biomolecules.
Authors: Lee, B.Y.T. / Sullivan, M.P. / Yano, E. / Tong, K.K.H. / Hanif, M. / Kawakubo-Yasukochi, T. / Jamieson, S.M.F. / Soehnel, T. / Goldstone, D.C. / Hartinger, C.G.
History
DepositionApr 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9175
Polymers14,3311
Non-polymers5854
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, None
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.305, 78.305, 38.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Lysozyme /


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: B8YK79, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-U0J / {(2R)-1-[(anthracen-9-yl)methyl]-3-methyl-2,3-dihydro-1H-imidazol-2-yl}(dichloro)ruthenium


Mass: 444.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16Cl2N2Ru / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 0.1 M Sodium Acetate pH 4.7 and 0.8 M Sodium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.3→38.03 Å / Num. obs: 29702 / % possible obs: 100 % / Redundancy: 26 % / CC1/2: 0.996 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.037 / Rrim(I) all: 0.19 / Net I/σ(I): 9.7 / Num. measured all: 773432 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.3-1.3225.85.743650614170.3811.1375.8540.7100
7.12-38.0319.80.12946792360.990.030.13322.199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.66 Å35.02 Å
Translation4.66 Å35.02 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.25data extraction
ARP/wARP7.6, patch 1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NHI

4nhi


Resolution: 1.3→35.04 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.2005 / WRfactor Rwork: 0.1499 / FOM work R set: 0.7252 / SU B: 3.247 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0525 / SU Rfree: 0.0525 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1924 1449 4.9 %RANDOM
Rwork0.1508 ---
obs0.1529 28202 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.27 Å2 / Biso mean: 20.102 Å2 / Biso min: 11.19 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å20 Å20 Å2
2--2.52 Å20 Å2
3----5.03 Å2
Refinement stepCycle: final / Resolution: 1.3→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 33 96 1130
Biso mean--26.97 32.01 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131142
X-RAY DIFFRACTIONr_bond_other_d0.0030.0181031
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.681559
X-RAY DIFFRACTIONr_angle_other_deg1.4951.6122379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.9319.275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79715195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7141517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021339
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02298
X-RAY DIFFRACTIONr_rigid_bond_restr2.75132172
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 106 -
Rwork0.34 2035 -
all-2141 -
obs--100 %

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