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

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Basic information

Entry
Database: PDB / ID: 7pni
TitleX-ray structure of the adduct formed upon reaction of Pt(II) complex 2c with ribonuclease A
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsRNA BINDING PROTEIN / metallodrug / platinum / protein interaction / Pt-protein adduct
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / 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
: / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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

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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)28,3927
Polymers27,4172
Non-polymers9755
Water2,504139
1
AAA: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2944
Polymers13,7081
Non-polymers5853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0983
Polymers13,7081
Non-polymers3902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.140, 31.790, 73.740
Angle α, β, γ (deg.)90.000, 90.347, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonuclease pancreatic / Pancreatic ribonuclease family / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG4K 10 mM 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: 0.96 Å
DetectorType: DECTRIS PILATUS 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: 2.13→28.04 Å / Num. obs: 13153 / % possible obs: 99 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Net I/σ(I): 14.5
Reflection shellResolution: 2.13→2.17 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 649 / CC1/2: 0.898 / Rpim(I) all: 0.318 / Rrim(I) all: 0.721 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jvt

1jvt


Resolution: 2.13→28.04 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.903 / SU B: 7.018 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / ESU R: 0.296 / ESU R Free: 0.245
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.275 674 5.134 %
Rwork0.1923 12454 -
all0.197 --
obs-13128 98.183 %
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: 39.806 Å2
Baniso -1Baniso -2Baniso -3
1--0.143 Å20 Å2-0.192 Å2
2---0.072 Å20 Å2
3---0.217 Å2
Refinement stepCycle: LAST / Resolution: 2.13→28.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 5 139 2029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131968
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181675
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0040.019
X-RAY DIFFRACTIONr_angle_refined_deg2.1951.6752679
X-RAY DIFFRACTIONr_angle_other_deg1.3221.5783937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7755254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31623.91897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55315333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.093158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022267
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02382
X-RAY DIFFRACTIONr_nbd_refined0.2060.2395
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.21575
X-RAY DIFFRACTIONr_nbtor_refined0.160.2930
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2877
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1360.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.219
X-RAY DIFFRACTIONr_nbd_other0.2230.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.219
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0280.21
X-RAY DIFFRACTIONr_mcbond_it3.9124.1611010
X-RAY DIFFRACTIONr_mcbond_other3.9134.1591009
X-RAY DIFFRACTIONr_mcangle_it6.1096.2021268
X-RAY DIFFRACTIONr_mcangle_other6.1056.2051267
X-RAY DIFFRACTIONr_scbond_it4.1784.453954
X-RAY DIFFRACTIONr_scbond_other4.1744.453954
X-RAY DIFFRACTIONr_scangle_it6.6566.5341420
X-RAY DIFFRACTIONr_scangle_other6.4656.531414
X-RAY DIFFRACTIONr_lrange_it9.28349.2262140
X-RAY DIFFRACTIONr_lrange_other9.2849.1872129
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
2.13-2.1850.429340.2868160.2929630.7640.7888.26580.242
2.185-2.2440.307410.2578800.2599490.8150.83397.04950.225
2.244-2.3090.346380.2448660.2489240.8270.87997.83550.207
2.309-2.380.369470.2258520.2329010.8390.89599.7780.186
2.38-2.4570.367400.2028150.2098680.8270.89798.50230.171
2.457-2.5430.341410.2087800.2148220.8640.90899.87830.175
2.543-2.6380.303450.1827850.1888320.890.92799.75960.164
2.638-2.7450.291420.1817280.1867740.8910.93199.48320.166
2.745-2.8650.279500.1897000.1967510.9020.92499.86680.18
2.865-3.0040.284510.1916520.1987090.8850.92499.15370.184
3.004-3.1640.267400.1936560.1976970.9030.93299.85650.19
3.164-3.3530.245300.1786270.1816620.9370.94999.24470.184
3.353-3.5810.203200.1655830.1666080.9260.95799.17760.177
3.581-3.8630.301330.1755390.1825760.9020.9499.30560.197
3.863-4.2240.209170.1615070.1635250.9440.94499.80950.19
4.224-4.7090.168340.1534550.1544890.9670.9631000.186
4.709-5.4120.274270.1594130.1654440.9150.96299.09910.197
5.412-6.5670.14290.2243560.2223690.8940.92598.9160.278
6.567-9.0430.28220.2452640.2482940.8990.90397.27890.303
9.043-28.0420.446120.2571720.2681970.880.91893.4010.31

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