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- PDB-7r1q: X-ray structure of the adduct formed upon reaction of the gold(I)... -

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Basic information

Entry
Database: PDB / ID: 7r1q
TitleX-ray structure of the adduct formed upon reaction of the gold(I) N-heterocyclic carbene complex Au2 with lysozyme
ComponentsLysozyme
KeywordsHYDROLASE / metallodrug / protein-metal interaction / gold / carbene / anticancer
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsMerlino, A. / Ferraro, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Dalton Trans / Year: 2022
Title: Halo complexes of gold(I) containing glycoconjugate carbene ligands: synthesis, characterization, cytotoxicity and interaction with proteins and DNA model systems.
Authors: Annunziata, A. / Ferraro, G. / Cucciolito, M.E. / Imbimbo, P. / Tuzi, A. / Monti, D.M. / Merlino, A. / Ruffo, F.
History
DepositionFeb 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
AAA: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0005
Polymers14,3311
Non-polymers6694
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-8 kcal/mol
Surface area6470 Å2
Unit cell
Length a, b, c (Å)77.000, 77.000, 37.270
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
11AAA-329-

HOH

21AAA-355-

HOH

31AAA-363-

HOH

41AAA-484-

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: P00698, lysozyme
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0 M sodium formate 0.1 M hepes buffer pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.1→34.43 Å / Num. obs: 44982 / % possible obs: 95.6 % / Redundancy: 17.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.013 / Rrim(I) all: 0.062 / Net I/σ(I): 28.4
Reflection shellResolution: 1.1→1.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1372 / CC1/2: 0.635 / Rpim(I) all: 0.318 / Rrim(I) all: 0.637 / % possible all: 58.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193L

193l


Resolution: 1.1→34.43 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.972 / SU ML: 0.022 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.035
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.17 2238 5.04 %
Rwork0.1322 42171 -
all0.134 --
obs-44409 96.541 %
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: 16.618 Å2
Baniso -1Baniso -2Baniso -3
1-0.579 Å2-0 Å2-0 Å2
2--0.579 Å2-0 Å2
3----1.159 Å2
Refinement stepCycle: LAST / Resolution: 1.1→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 7 213 1221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0121184
X-RAY DIFFRACTIONr_bond_other_d0.0090.0181050
X-RAY DIFFRACTIONr_angle_refined_deg2.7081.6391624
X-RAY DIFFRACTIONr_angle_other_deg1.8761.5932431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.3285.219160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2542073
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98715199
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg28.186154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8011515
X-RAY DIFFRACTIONr_chiral_restr0.1580.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021490
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02295
X-RAY DIFFRACTIONr_nbd_refined0.2450.2304
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.21018
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2569
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1050.2483
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2124
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1110.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.215
X-RAY DIFFRACTIONr_nbd_other0.2580.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2590.255
X-RAY DIFFRACTIONr_mcbond_it8.0021.351592
X-RAY DIFFRACTIONr_mcbond_other7.9531.349592
X-RAY DIFFRACTIONr_mcangle_it6.9382.018764
X-RAY DIFFRACTIONr_mcangle_other6.9652.021765
X-RAY DIFFRACTIONr_scbond_it7.5911.78591
X-RAY DIFFRACTIONr_scbond_other7.5851.779592
X-RAY DIFFRACTIONr_scangle_it6.9832.521860
X-RAY DIFFRACTIONr_scangle_other6.9792.52861
X-RAY DIFFRACTIONr_lrange_it7.47818.3481526
X-RAY DIFFRACTIONr_lrange_other7.46717.271471
X-RAY DIFFRACTIONr_rigid_bond_restr17.52432232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.129-1.1590.1981330.1682687X-RAY DIFFRACTION86.8762
1.159-1.1930.1711550.1372953X-RAY DIFFRACTION97.9206
1.193-1.230.171670.1262887X-RAY DIFFRACTION99.1558
1.23-1.270.1411580.1132835X-RAY DIFFRACTION100
1.27-1.3150.1631470.1132754X-RAY DIFFRACTION99.9655
1.315-1.3640.1311350.112659X-RAY DIFFRACTION100
1.364-1.420.1461460.112578X-RAY DIFFRACTION100
1.42-1.4830.1331100.1082482X-RAY DIFFRACTION100
1.483-1.5550.1531300.1122380X-RAY DIFFRACTION100
1.555-1.6390.1181290.1052230X-RAY DIFFRACTION100
1.639-1.7390.1441220.112126X-RAY DIFFRACTION100
1.739-1.8590.1521100.1162029X-RAY DIFFRACTION100
1.859-2.0070.166940.121859X-RAY DIFFRACTION100
2.007-2.1990.166880.1221771X-RAY DIFFRACTION100
2.199-2.4580.141840.1271577X-RAY DIFFRACTION100
2.458-2.8370.198700.141426X-RAY DIFFRACTION100
2.837-3.4720.185610.1391215X-RAY DIFFRACTION100
3.472-4.90.2520.15960X-RAY DIFFRACTION100

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