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- PDB-6pl9: Adduct formed after 1 month in the reaction of dichlorido(1,3-dim... -

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Basic information

Entry
Database: PDB / ID: 6pl9
TitleAdduct formed after 1 month in the reaction of dichlorido(1,3-dimethylbenzimidaz ol-2-ylidene)(eta5-pentamethylcyclopentadienyl)rhodium(III) with HEWL
ComponentsLysozyme
KeywordsHYDROLASE / metal-based / anticancer / ruthenium / NHC / carbene / lysozyme / metallodrug / benzimidazole / dimethylbenzimidazole
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
Chem-ORS / Chem-R1N / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsSullivan, M.P. / Hartinger, C.G. / Goldstone, D.C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Probing the Paradigm of Promiscuity for N-Heterocyclic Carbene Complexes and their Protein Adduct Formation.
Authors: Sullivan, M.P. / Cziferszky, M. / Tolbatov, I. / Truong, D. / Mercadante, D. / Re, N. / Gust, R. / Goldstone, D.C. / Hartinger, C.
History
DepositionJun 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0834
Polymers14,3311
Non-polymers7523
Water2,432135
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)80.425, 80.425, 37.794
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-391-

HOH

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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-ORS / dichloro[(1,2,3,4,5-eta)-pentamethylcyclopentadienyl]rhodium


Mass: 309.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15Cl2Rh / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-R1N / 2-(1-chloranyl-2,3,4,5,6-pentamethyl-1$l^{7}-rhodapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexan-1-yl)-1,3-dimethyl-benzimidazole


Mass: 419.774 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25ClN2Rh / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.13 Å3/Da / Density % sol: 42.31 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Rh(III)(Cp*)(1,3-dimethylbenzimidazol-2-ylidene)(Cl)2 (1.09 mg, 1 mg/mL) soak occurred in 0.8 M ...Details: Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Rh(III)(Cp*)(1,3-dimethylbenzimidazol-2-ylidene)(Cl)2 (1.09 mg, 1 mg/mL) soak occurred in 0.8 M sodium nitrate and 0.1 M sodium acetate pH 4.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.2→37.79 Å / Num. obs: 39348 / % possible obs: 100 % / Redundancy: 14.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.018 / Rrim(I) all: 0.066 / Net I/σ(I): 22.5 / Num. measured all: 552879 / Scaling rejects: 323
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
1.2-1.2212.23.7742315819020.3121.1183.940.7100
6.57-37.79110.04933763080.9980.0150.05173.499.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.71 Å35.97 Å
Translation4.71 Å35.97 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.8.2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NHI

4nhi


Resolution: 1.2→35.99 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1919 / WRfactor Rwork: 0.1626 / FOM work R set: 0.7677 / SU B: 1.939 / SU ML: 0.036 / SU R Cruickshank DPI: 0.045 / SU Rfree: 0.0446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2027 1998 5.1 %RANDOM
Rwork0.172 ---
obs0.1735 37290 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.16 Å2 / Biso mean: 17.316 Å2 / Biso min: 10.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20 Å2
2--1.43 Å20 Å2
3----2.86 Å2
Refinement stepCycle: final / Resolution: 1.2→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 37 135 1173
Biso mean--23.97 31.99 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131116
X-RAY DIFFRACTIONr_bond_other_d0.0010.018996
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.7431579
X-RAY DIFFRACTIONr_angle_other_deg1.4331.6392288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7265140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4962069
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5415179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8831514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
X-RAY DIFFRACTIONr_rigid_bond_restr1.11332110
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 171 -
Rwork0.435 2664 -
all-2835 -
obs--99.96 %

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