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- PDB-7pnh: X-ray structure of the adduct formed upon reaction of Pt(II) comp... -

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Basic information

Entry
Database: PDB / ID: 7pnh
TitleX-ray structure of the adduct formed upon reaction of Pt(II) complex 2c with lysozyme
ComponentsLysozyme
KeywordsHYDROLASE / metallodrug / platinum / protein interaction / Pt-protein adduct
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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
IMIDAZOLE / NITRATE ION / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsFerraro, G. / Merlino, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2021
Title: Reactions with Proteins of Three Novel Anticancer Platinum(II) Complexes Bearing N-Heterocyclic Ligands.
Authors: Sacco, F. / Tarchi, M. / Ferraro, G. / Merlino, A. / Facchetti, G. / Rimoldi, I. / Messori, L. / Massai, L.
History
DepositionSep 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,45714
Polymers14,3311
Non-polymers1,12613
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-14 kcal/mol
Surface area6270 Å2
Unit cell
Length a, b, c (Å)77.200, 77.200, 38.530
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
11AAA-322-

HOH

21AAA-347-

HOH

31AAA-437-

HOH

41AAA-475-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#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

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Non-polymers , 6 types, 190 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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 Å3/Da / Density % sol: 38.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% ethylene glycol 0.1 M sodium acetate buffer pH 4.0 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: 0.96 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.22→34.52 Å / Num. obs: 35283 / % possible obs: 100 % / Redundancy: 23.2 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.012 / Rrim(I) all: 0.057 / Net I/σ(I): 24.5
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 24.3 % / Rmerge(I) obs: 1.531 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1737 / CC1/2: 0.861 / Rpim(I) all: 0.315 / Rrim(I) all: 1.564 / % possible all: 100

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Processing

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

193l


Resolution: 1.22→34.52 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.559 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.043
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1741 1687 4.962 %
Rwork0.1328 32310 -
all0.135 --
obs-33997 96.489 %
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: 20.279 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å2-0 Å2-0 Å2
2--0.52 Å2-0 Å2
3----1.039 Å2
Refinement stepCycle: LAST / Resolution: 1.22→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 49 177 1227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131110
X-RAY DIFFRACTIONr_bond_other_d0.0180.018971
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0410.013
X-RAY DIFFRACTIONr_angle_refined_deg2.2731.6741499
X-RAY DIFFRACTIONr_angle_other_deg1.9171.5922244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3125136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55320.61565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02415180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7681512
X-RAY DIFFRACTIONr_chiral_restr0.140.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021308
X-RAY DIFFRACTIONr_gen_planes_other0.010.02264
X-RAY DIFFRACTIONr_nbd_refined0.2260.2275
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.2949
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2539
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2530.2106
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0930.21
X-RAY DIFFRACTIONr_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2680.214
X-RAY DIFFRACTIONr_nbd_other0.2460.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.219
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0580.21
X-RAY DIFFRACTIONr_mcbond_it1.7881.675534
X-RAY DIFFRACTIONr_mcbond_other1.7341.674534
X-RAY DIFFRACTIONr_mcangle_it2.2152.535675
X-RAY DIFFRACTIONr_mcangle_other2.2172.538675
X-RAY DIFFRACTIONr_scbond_it4.4922.173575
X-RAY DIFFRACTIONr_scbond_other4.4882.173576
X-RAY DIFFRACTIONr_scangle_it4.8473.088826
X-RAY DIFFRACTIONr_scangle_other4.8443.088827
X-RAY DIFFRACTIONr_lrange_it5.4623.0221379
X-RAY DIFFRACTIONr_lrange_other5.45823.0321380
X-RAY DIFFRACTIONr_rigid_bond_restr8.90932079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.2520.263790.2451820X-RAY DIFFRACTION74.064
1.252-1.2860.275960.2342001X-RAY DIFFRACTION83.2804
1.286-1.3230.272980.2172166X-RAY DIFFRACTION94.6884
1.323-1.3640.2161310.2022227X-RAY DIFFRACTION99.3679
1.364-1.4090.2411080.182163X-RAY DIFFRACTION100
1.409-1.4580.1981080.1552120X-RAY DIFFRACTION100
1.458-1.5130.1731110.1242042X-RAY DIFFRACTION100
1.513-1.5750.1841060.1111962X-RAY DIFFRACTION100
1.575-1.6450.17920.11881X-RAY DIFFRACTION100
1.645-1.7250.163980.1011815X-RAY DIFFRACTION100
1.725-1.8180.144940.1011725X-RAY DIFFRACTION99.9451
1.818-1.9280.18810.111652X-RAY DIFFRACTION100
1.928-2.0610.143800.111532X-RAY DIFFRACTION100
2.061-2.2260.165780.1151447X-RAY DIFFRACTION100
2.226-2.4380.163710.1071330X-RAY DIFFRACTION100
2.438-2.7250.192760.1151211X-RAY DIFFRACTION100
2.725-3.1460.14650.1211072X-RAY DIFFRACTION100
3.146-3.8490.143530.121941X-RAY DIFFRACTION100
3.849-5.430.156340.149744X-RAY DIFFRACTION100

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