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- PDB-9hn6: X-ray structure of the adduct formed upon reaction of the diiodid... -

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Basic information

Entry
Database: PDB / ID: 9hn6
TitleX-ray structure of the adduct formed upon reaction of the diiodido analogue of picoplatin with ribonuclease A
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / platin / interaction / metallodrug / picoplatin / diiodido analogue / ribonuclease
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
IODIDE ION / AMMONIA / : / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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 10, 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: Ribonuclease pancreatic
BBB: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,35932
Polymers27,4172
Non-polymers3,94330
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-302 kcal/mol
Surface area12290 Å2
Unit cell
Length a, b, c (Å)100.040, 32.640, 73.450
Angle α, β, γ (deg.)90.000, 90.109, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61823, pancreatic ribonuclease

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Non-polymers , 5 types, 167 molecules

#2: Chemical
ChemComp-NH3 / AMMONIA


Mass: 17.031 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NH3
#3: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 20% PEG4000, and 0.1 M sodium citrate pH 5.1

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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: 1.77→73.45 Å / Num. obs: 23489 / % possible obs: 99.7 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.035 / Rrim(I) all: 0.085 / Net I/σ(I): 12
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6936 / CC1/2: 0.86 / Rpim(I) all: 0.393 / Rrim(I) all: 0.966 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→73.45 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.329 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.143 / ESU R Free: 0.151
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2761 1094 4.674 %
Rwork0.208 22312 -
all0.211 --
obs-23406 99.254 %
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: 34.929 Å2
Baniso -1Baniso -2Baniso -3
1--0.146 Å20 Å2-0.075 Å2
2--0.09 Å20 Å2
3---0.057 Å2
Refinement stepCycle: LAST / Resolution: 1.77→73.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 30 137 2019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131928
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181642
X-RAY DIFFRACTIONr_ext_dist_refined_d0.1090.0139
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6582653
X-RAY DIFFRACTIONr_angle_other_deg1.421.583858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0475245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06523.87898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38115327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.891158
X-RAY DIFFRACTIONr_chiral_restr0.0720.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212231
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02375
X-RAY DIFFRACTIONr_nbd_refined0.250.2402
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.21576
X-RAY DIFFRACTIONr_nbtor_refined0.1570.2931
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3170.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0410.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.216
X-RAY DIFFRACTIONr_nbd_other0.1910.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2430.218
X-RAY DIFFRACTIONr_mcbond_it2.783.573980
X-RAY DIFFRACTIONr_mcbond_other2.7713.571979
X-RAY DIFFRACTIONr_mcangle_it4.2755.3191232
X-RAY DIFFRACTIONr_mcangle_other4.2685.321230
X-RAY DIFFRACTIONr_scbond_it3.5243.905944
X-RAY DIFFRACTIONr_scbond_other3.523.904944
X-RAY DIFFRACTIONr_scangle_it6.1825.7221460
X-RAY DIFFRACTIONr_scangle_other5.9285.7061429
X-RAY DIFFRACTIONr_lrange_it8.15642.6242137
X-RAY DIFFRACTIONr_lrange_other8.10942.4632106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.8160.306830.2641576X-RAY DIFFRACTION95.2901
1.816-1.8660.285700.251565X-RAY DIFFRACTION99.5131
1.866-1.920.29880.2331577X-RAY DIFFRACTION99.5218
1.92-1.9790.238980.2341450X-RAY DIFFRACTION99.4859
1.979-2.0440.298580.2191504X-RAY DIFFRACTION99.4904
2.044-2.1150.277670.2121414X-RAY DIFFRACTION99.6635
2.115-2.1950.282710.2041372X-RAY DIFFRACTION99.7236
2.195-2.2850.274530.2121311X-RAY DIFFRACTION99.562
2.285-2.3860.305570.2191272X-RAY DIFFRACTION99.3274
2.386-2.5020.249500.2141257X-RAY DIFFRACTION100
2.502-2.6380.298600.2151125X-RAY DIFFRACTION99.5798
2.638-2.7970.223630.2121084X-RAY DIFFRACTION99.7391
2.797-2.990.257450.2011039X-RAY DIFFRACTION99.6324
2.99-3.2290.225360.202977X-RAY DIFFRACTION99.9014
3.229-3.5370.266510.189877X-RAY DIFFRACTION99.5708
3.537-3.9530.242390.178800X-RAY DIFFRACTION98.9387
3.953-4.5630.228280.163730X-RAY DIFFRACTION99.7368
4.563-5.5830.267410.182611X-RAY DIFFRACTION100
5.583-7.8720.332230.242478X-RAY DIFFRACTION99.2079

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