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- PDB-8c3b: X-ray structure of RNase A upon reaction with a Ruthenium(II)-are... -

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Basic information

Entry
Database: PDB / ID: 8c3b
TitleX-ray structure of RNase A upon reaction with a Ruthenium(II)-arene Complexed with Glycosylated Carbene Ligands (5)
ComponentsRibonuclease pancreatic
KeywordsRNA BINDING PROTEIN / ruthenium / carbene / protein binding
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
Chem-R6U / Chem-T9L / Chem-T9U / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsFerraro, G. / Merlino, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Organometallics / Year: 2023
Title: Ruthenium(II)–Arene Complexes with Glycosylated NHC-Carbene Co-Ligands: Synthesis, Hydrolytic Behavior, and Binding to Biological Molecules
Authors: Annunziata, A. / Cucciolito, M.E. / Di Ronza, M. / Ferraro, G. / Hadiji, M. / Merlino, A. / Ortiz, D. / Scopelliti, R. / Fadaei Tirani, F. / Dyson, P.J. / Ruffo, F.
History
DepositionDec 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 13, 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

Downloads & links

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Assembly

Deposited unit
AAA: Ribonuclease pancreatic
BBB: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2576
Polymers27,4172
Non-polymers8414
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-16 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.740, 32.920, 72.630
Angle α, β, γ (deg.)90.000, 90.008, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11BBB-427-

HOH

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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, 326 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-R6U / (1,3-dimethylimidazol-1-ium-2-yl)-tris(oxidanyl)ruthenium


Mass: 248.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11N2O3Ru / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-T9L / (1,3-dimethylimidazol-1-ium-2-yl)-tetrakis(oxidanyl)ruthenium


Mass: 265.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O4Ru / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-T9U / (1,3-dimethyl-2~{H}-imidazol-2-yl)-oxidanyl-oxidanylidene-ruthenium


Mass: 231.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O2Ru / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.2 Å3/Da / Density % sol: 44 %
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: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→72.63 Å / Num. obs: 59589 / % possible obs: 99.2 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Net I/σ(I): 21.7
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2458 / CC1/2: 0.763 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jvt

1jvt


Resolution: 1.24→72.63 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.127 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.061
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2269 2940 4.934 %
Rwork0.1916 56649 -
all0.193 --
obs-59589 87.982 %
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: 26.745 Å2
Baniso -1Baniso -2Baniso -3
1--0.026 Å2-0 Å2-0.066 Å2
2--0.078 Å2-0 Å2
3----0.052 Å2
Refinement stepCycle: LAST / Resolution: 1.24→72.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 38 322 2262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132096
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151832
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.6652845
X-RAY DIFFRACTIONr_angle_other_deg1.5081.594260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1985272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09524.369103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21415361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.328158
X-RAY DIFFRACTIONr_chiral_restr0.080.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022503
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02475
X-RAY DIFFRACTIONr_nbd_refined0.2370.2411
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21695
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2989
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2964
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2188
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.217
X-RAY DIFFRACTIONr_nbd_other0.2190.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.254
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0250.21
X-RAY DIFFRACTIONr_mcbond_it2.5332.5871055
X-RAY DIFFRACTIONr_mcbond_other2.5332.5871054
X-RAY DIFFRACTIONr_mcangle_it3.9663.8721338
X-RAY DIFFRACTIONr_mcangle_other3.9653.8721339
X-RAY DIFFRACTIONr_scbond_it2.9982.8121040
X-RAY DIFFRACTIONr_scbond_other2.9462.8061003
X-RAY DIFFRACTIONr_scangle_it4.6294.0911507
X-RAY DIFFRACTIONr_scangle_other4.5914.0821466
X-RAY DIFFRACTIONr_lrange_it7.78331.8462366
X-RAY DIFFRACTIONr_lrange_other7.6631.0832269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.389-1.4340.3172360.2794175X-RAY DIFFRACTION98.7022
1.434-1.4850.2742210.2494022X-RAY DIFFRACTION98.8123
1.485-1.5410.2692030.2413855X-RAY DIFFRACTION99.0723
1.541-1.6030.2422360.2223771X-RAY DIFFRACTION99.1586
1.603-1.6750.2281710.2043604X-RAY DIFFRACTION99.4206
1.675-1.7560.2461790.2033503X-RAY DIFFRACTION99.2988
1.756-1.8510.2251610.2013308X-RAY DIFFRACTION99.4838
1.851-1.9640.2411510.1973146X-RAY DIFFRACTION99.3372
1.964-2.0990.2231490.1912948X-RAY DIFFRACTION99.7102
2.099-2.2670.2021240.1852775X-RAY DIFFRACTION99.4511
2.267-2.4830.2291380.182514X-RAY DIFFRACTION99.6243
2.483-2.7760.2261370.1822275X-RAY DIFFRACTION99.2184
2.776-3.2050.216950.1772065X-RAY DIFFRACTION99.631
3.205-3.9230.205930.1631733X-RAY DIFFRACTION99.1852
3.923-5.540.186640.1491350X-RAY DIFFRACTION98.5366

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