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- PDB-9eo5: X-ray structure of the adduct formed upon reaction of picoplatin ... -

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Basic information

Entry
Database: PDB / ID: 9eo5
TitleX-ray structure of the adduct formed upon reaction of picoplatin with bovine pancreatic ribonuclease (structure C)
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsRNA BINDING PROTEIN / picoplatin / lysozyme / protein / interaction
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / nucleic acid binding / 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
AMMONIA / : / Ribonuclease pancreatic
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsFerraro, G. / Merlino, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Dalton Trans / Year: 2024
Title: Picoplatin binding to proteins: X-ray structures and mass spectrometry data on the adducts with lysozyme and ribonuclease A.
Authors: Ferraro, G. / Lyckova, T. / Massai, L. / Starha, P. / Messori, L. / Merlino, A.
History
DepositionMar 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)28,47712
Polymers27,4172
Non-polymers1,06110
Water3,459192
1
AAA: Ribonuclease pancreatic
hetero molecules


  • defined by author
  • 14.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,1335
Polymers13,7081
Non-polymers4244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Ribonuclease pancreatic
hetero molecules


  • defined by author
  • 14.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,3457
Polymers13,7081
Non-polymers6366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.750, 32.690, 73.540
Angle α, β, γ (deg.)90.000, 90.463, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11BBB-331-

HOH

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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) Gallus gallus (chicken) / References: UniProt: P61824, pancreatic ribonuclease
#2: Chemical
ChemComp-NH3 / AMMONIA / Ammonia


Mass: 17.031 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NH3
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 22% PEG4000, 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 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50.424 Å / Num. obs: 16745 / % possible obs: 99.8 % / Redundancy: 5.9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.161 / Net I/σ(I): 7.3
Reflection shellResolution: 1.99→2.08 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 844 / CC1/2: 0.638 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→50.424 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.858 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.212 / ESU R Free: 0.182
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2426 755 4.544 %
Rwork0.1909 15862 -
all0.193 --
obs-16617 98.641 %
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: 32.756 Å2
Baniso -1Baniso -2Baniso -3
1-0.101 Å2-0 Å20.134 Å2
2--0.077 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.99→50.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 10 192 2096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132008
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181706
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0130.0117
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.652748
X-RAY DIFFRACTIONr_angle_other_deg1.3671.584013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5715261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64324100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7115340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.212158
X-RAY DIFFRACTIONr_chiral_restr0.0630.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022334
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02391
X-RAY DIFFRACTIONr_nbd_refined0.2240.2449
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.21599
X-RAY DIFFRACTIONr_nbtor_refined0.160.2938
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2897
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2177
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0130.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1780.223
X-RAY DIFFRACTIONr_nbd_other0.2230.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2270.215
X-RAY DIFFRACTIONr_mcbond_it2.7353.4771029
X-RAY DIFFRACTIONr_mcbond_other2.7363.4771028
X-RAY DIFFRACTIONr_mcangle_it4.2595.1881301
X-RAY DIFFRACTIONr_mcangle_other4.2625.1881299
X-RAY DIFFRACTIONr_scbond_it2.983.61979
X-RAY DIFFRACTIONr_scbond_other2.9783.61979
X-RAY DIFFRACTIONr_scangle_it4.8025.311464
X-RAY DIFFRACTIONr_scangle_other4.6875.3031455
X-RAY DIFFRACTIONr_lrange_it7.71240.6662277
X-RAY DIFFRACTIONr_lrange_other7.63940.4452225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.0420.221390.2461058X-RAY DIFFRACTION87.4104
2.042-2.0980.268520.2281074X-RAY DIFFRACTION95.9114
2.098-2.1580.249440.2291115X-RAY DIFFRACTION99.3145
2.158-2.2250.224440.2071083X-RAY DIFFRACTION99.9113
2.225-2.2980.232460.21072X-RAY DIFFRACTION100
2.298-2.3780.232340.2111008X-RAY DIFFRACTION99.9041
2.378-2.4680.302630.203960X-RAY DIFFRACTION99.9023
2.468-2.5680.278470.206939X-RAY DIFFRACTION99.7976
2.568-2.6830.311470.198925X-RAY DIFFRACTION100
2.683-2.8130.287510.204854X-RAY DIFFRACTION100
2.813-2.9650.22360.18839X-RAY DIFFRACTION99.8858
2.965-3.1450.306400.187765X-RAY DIFFRACTION99.8759
3.145-3.3610.294300.18757X-RAY DIFFRACTION100
3.361-3.630.242270.185707X-RAY DIFFRACTION100
3.63-3.9760.209270.182621X-RAY DIFFRACTION99.6923
3.976-4.4430.192420.151582X-RAY DIFFRACTION100
4.443-5.1280.22260.15505X-RAY DIFFRACTION100
5.128-6.2720.206240.173444X-RAY DIFFRACTION100
6.272-8.8380.268240.193349X-RAY DIFFRACTION100
8.838-50.4240.167120.241200X-RAY DIFFRACTION97.6959

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