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- PDB-9gys: X-ray structure of the adduct formed upon reaction of RNase A wit... -

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Basic information

Entry
Database: PDB / ID: 9gys
TitleX-ray structure of the adduct formed upon reaction of RNase A with [Ru2(D-p-FPhF)(O2CCH3)2(O2CO)] complex
ComponentsRibonuclease pancreatic
KeywordsSTRUCTURAL PROTEIN / Diruthenium / protein interaction / metallodrug
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
: / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsTeran, A. / Ferraro, G. / Merlino, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Deciphering the role of neutral diruthenium complexes in protein binding.
Authors: Ferraro, G. / Teran, A. / Galardo, F. / Lucignano, R. / Picone, D. / Massai, L. / Fasulo, F. / Munoz-Garcia, A.B. / Messori, L. / Herrero, S. / Merlino, A.
History
DepositionOct 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5708
Polymers27,4172
Non-polymers3,1536
Water3,927218
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6395
Polymers13,7081
Non-polymers1,9304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9313
Polymers13,7081
Non-polymers1,2232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.540, 32.600, 72.350
Angle α, β, γ (deg.)90.000, 90.014, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-305-

HOH

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Components

#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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-A1IQW / [Ru2-N,N'-diphenylformamidinate(O2CCH3)2(O2CO)] complex / Diruthenium complex


Mass: 611.458 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H15F2N2O7Ru2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG4K, 10 mM sodium citrate buffer at 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: Jul 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→50.27 Å / Num. obs: 23214 / % possible obs: 94.4 % / Redundancy: 2.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.6
Reflection shellResolution: 1.74→1.77 Å / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1137 / CC1/2: 0.745

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→50.27 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.169 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.147 / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1160 5.058 %0.261
Rwork0.1922 21772 --
all0.195 ---
obs-22932 93.486 %-
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: 25.606 Å2
Baniso -1Baniso -2Baniso -3
1--0.082 Å20 Å20.147 Å2
2--0.084 Å2-0 Å2
3----0.002 Å2
Refinement stepCycle: LAST / Resolution: 1.74→50.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 78 218 2194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122092
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161777
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.8632871
X-RAY DIFFRACTIONr_angle_other_deg0.5521.784124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1175262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.71858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68910343
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.8961091
X-RAY DIFFRACTIONr_chiral_restr0.0770.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02456
X-RAY DIFFRACTIONr_nbd_refined0.1910.2437
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.21695
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2986
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21041
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2194
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.220
X-RAY DIFFRACTIONr_nbd_other0.170.298
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.248
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1250.21
X-RAY DIFFRACTIONr_mcbond_it2.6412.7391030
X-RAY DIFFRACTIONr_mcbond_other2.6412.7391030
X-RAY DIFFRACTIONr_mcangle_it4.0034.8971298
X-RAY DIFFRACTIONr_mcangle_other4.0024.8961299
X-RAY DIFFRACTIONr_scbond_it2.9333.0061062
X-RAY DIFFRACTIONr_scbond_other2.8272.934985
X-RAY DIFFRACTIONr_scangle_it4.565.4841573
X-RAY DIFFRACTIONr_scangle_other4.5575.2631444
X-RAY DIFFRACTIONr_lrange_it7.3531.4762423
X-RAY DIFFRACTIONr_lrange_other7.12228.9082302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.7850.354860.2771395X-RAY DIFFRACTION83.4366
1.785-1.8340.238740.2381576X-RAY DIFFRACTION93.5905
1.834-1.8870.324920.2411547X-RAY DIFFRACTION96.2419
1.887-1.9450.2491060.2131448X-RAY DIFFRACTION92.8315
1.945-2.0090.293610.2151431X-RAY DIFFRACTION95.7024
2.009-2.0790.22780.1921416X-RAY DIFFRACTION95.6466
2.079-2.1580.219780.1871354X-RAY DIFFRACTION96.0429
2.158-2.2450.272650.1941315X-RAY DIFFRACTION95.5017
2.245-2.3450.262620.2011251X-RAY DIFFRACTION93.0546
2.345-2.4590.262640.1851162X-RAY DIFFRACTION94.1628
2.459-2.5920.269650.1851141X-RAY DIFFRACTION94.5141
2.592-2.7490.264540.1831084X-RAY DIFFRACTION94.9917
2.749-2.9380.258510.1781035X-RAY DIFFRACTION94.1891
2.938-3.1720.254480.181942X-RAY DIFFRACTION94.9185
3.172-3.4740.23540.172844X-RAY DIFFRACTION93.3472
3.474-3.8810.285260.16798X-RAY DIFFRACTION91.8618
3.881-4.4770.247500.153666X-RAY DIFFRACTION91.6773
4.477-5.4730.195130.181612X-RAY DIFFRACTION92.8678
5.473-7.6940.297240.228463X-RAY DIFFRACTION91.3696
7.694-50.270.34690.277290X-RAY DIFFRACTION92.5697

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