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- PDB-9hlk: X-ray structure of the adduct formed upon reaction of the diiodid... -

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Basic information

Entry
Database: PDB / ID: 9hlk
TitleX-ray structure of the adduct formed upon reaction of the diiodido analogue of picoplatin with lysozyme (structure A)
ComponentsLysozyme C
KeywordsHYDROLASE / metallodrug / picoplatin / analogue / diiodido / protein-metal interaction
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
ACETATE ION / IODIDE ION / AMMONIA / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsFerraro, G. / Merlino, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)2022JMFC3X Italy
CitationJournal: Inorg.Chem. / Year: 2025
Title: Cytotoxicity and Binding to DNA, Lysozyme, Ribonuclease A, and Human Serum Albumin of the Diiodido Analog of Picoplatin.
Authors: Ferraro, G. / Pracharova, J. / Gotte, G. / Massai, L. / Berecka, M. / Starha, P. / Messori, L. / Merlino, A.
History
DepositionDec 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,55312
Polymers14,3311
Non-polymers1,22111
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-80 kcal/mol
Surface area6380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.400, 78.400, 36.920
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-311-

HOH

21AAA-313-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#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

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Non-polymers , 6 types, 83 molecules

#2: Chemical ChemComp-NH3 / AMMONIA


Mass: 17.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NH3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.1 M sodium chloride 0.1 M sodium acetate buffer pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→55.44 Å / Num. obs: 8548 / % possible obs: 98.6 % / Redundancy: 20.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.015 / Rrim(I) all: 0.069 / Net I/σ(I): 29.9
Reflection shellResolution: 1.96→2 Å / Redundancy: 23.3 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 381 / CC1/2: 0.969 / Rpim(I) all: 0.204 / Rrim(I) all: 0.987 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→55.437 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.276 / SU ML: 0.176 / Cross valid method: FREE R-VALUE / ESU R: 0.232 / ESU R Free: 0.201
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2691 412 4.827 %
Rwork0.2057 8124 -
all0.209 --
obs-8536 98.205 %
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: 40.371 Å2
Baniso -1Baniso -2Baniso -3
1--0.197 Å20 Å20 Å2
2---0.197 Å20 Å2
3---0.394 Å2
Refinement stepCycle: LAST / Resolution: 1.96→55.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 14 72 1087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131078
X-RAY DIFFRACTIONr_bond_other_d0.0010.018950
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0110.018
X-RAY DIFFRACTIONr_angle_refined_deg1.761.6391478
X-RAY DIFFRACTIONr_angle_other_deg1.4121.5882195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3815136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28920.44168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90815177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9421513
X-RAY DIFFRACTIONr_chiral_restr0.0790.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021281
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02264
X-RAY DIFFRACTIONr_nbd_refined0.2070.2288
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.2967
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2523
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2460
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.255
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.280.28
X-RAY DIFFRACTIONr_nbd_other0.2680.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.28
X-RAY DIFFRACTIONr_mcbond_it44.048536
X-RAY DIFFRACTIONr_mcbond_other3.8774.023534
X-RAY DIFFRACTIONr_mcangle_it5.5386.031675
X-RAY DIFFRACTIONr_mcangle_other5.5976.05675
X-RAY DIFFRACTIONr_scbond_it4.5454.527542
X-RAY DIFFRACTIONr_scbond_other4.5434.527543
X-RAY DIFFRACTIONr_scangle_it7.5616.698811
X-RAY DIFFRACTIONr_scangle_other7.4486.677808
X-RAY DIFFRACTIONr_lrange_it10.34448.4991334
X-RAY DIFFRACTIONr_lrange_other10.34748.4441327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.96-2.0110.385330.2115410.2226240.8740.93891.98720.177
2.011-2.0660.426230.3045880.3086130.7010.76199.67370.257
2.066-2.1260.387320.35470.3055830.7050.71599.31390.261
2.126-2.1910.314270.3155480.3155760.6470.68399.82640.271
2.191-2.2630.566250.4614950.4675620.740.7792.52670.398
2.263-2.3420.25200.2724960.2715560.8940.85192.80580.238
2.342-2.430.293270.2354880.2395150.880.8981000.213
2.43-2.5290.277240.2164880.2195130.860.89999.80510.198
2.529-2.6420.333210.2274750.2324970.8820.90199.79880.214
2.642-2.770.302250.2364290.244550.8430.89299.78020.232
2.77-2.920.3170.2194350.2234520.9020.9091000.227
2.92-3.0960.384240.2094120.2164360.8960.9171000.224
3.096-3.3090.219230.1843690.1863920.9310.9421000.211
3.309-3.5730.272170.1853650.1893820.9220.9511000.203
3.573-3.9130.21200.163270.1633470.9610.9631000.179
3.913-4.3720.237150.133030.1353180.9470.9751000.166
4.372-5.0430.145120.1572770.1562890.9790.9671000.21
5.043-6.1630.167130.1712410.1712550.9580.96299.60780.207
6.163-8.6630.16980.1751890.1751970.9620.9671000.214
8.663-55.4370.41560.1961110.2021300.9340.967900.248

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