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- PDB-7qq0: X-ray structure of the adduct obtained upon reaction of [cis-Rh2(... -

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Basic information

Entry
Database: PDB / ID: 7qq0
TitleX-ray structure of the adduct obtained upon reaction of [cis-Rh2(OCOCH3)2(OCOCF3)2] with RNase A (2)
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Protein metalation / dirhodium tetraacetate derivative / dimetallic paddlewheel complexes
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
(mi2-acetato-O, O')-hexaaquo-dirhodium (II) / RHODIUM(II) ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsLoreto, D. / Merlino, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Not funded Italy
CitationJournal: Dalton Trans / Year: 2022
Title: Reactivity of a fluorine-containing dirhodium tetracarboxylate compound with proteins.
Authors: Loreto, D. / Esposito, A. / Demitri, N. / Guaragna, A. / Merlino, A.
History
DepositionJan 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,3586
Polymers27,4172
Non-polymers9424
Water6,972387
1
AAA: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2824
Polymers13,7081
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0762
Polymers13,7081
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.210, 32.560, 72.610
Angle α, β, γ (deg.)90.000, 90.309, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-416-

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-F3I / (mi2-acetato-O, O')-hexaaquo-dirhodium (II)


Mass: 367.907 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H10O8Rh2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-RHF / RHODIUM(II) ION


Mass: 102.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Rh
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
22.1643.06
1
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG 4K 10 mM sodium citrate buffer 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: May 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→41.143 Å / Num. obs: 54908 / % possible obs: 99.5 % / Redundancy: 5.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.1 / Net I/σ(I): 10.8
Reflection shellResolution: 1.32→1.35 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.862 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2752 / CC1/2: 0.704 / Rpim(I) all: 0.57 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JVT

1jvt


Resolution: 1.32→41.14 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.89 / SU B: 1.088 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.067 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.243 2648 4.79 %
Rwork0.2088 52631 -
all0.21 --
obs-54908 99.471 %
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: 15.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.032 Å20 Å20.036 Å2
2--0.062 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.32→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 26 387 2315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132113
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181788
X-RAY DIFFRACTIONr_angle_refined_deg3.0981.6742891
X-RAY DIFFRACTIONr_angle_other_deg1.5451.5844222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6545277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65424.327104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2915368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.66158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022495
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02405
X-RAY DIFFRACTIONr_nbd_refined0.1980.2442
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21720
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21003
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2926
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.080.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.228
X-RAY DIFFRACTIONr_nbd_other0.1670.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1830.245
X-RAY DIFFRACTIONr_mcbond_it1.5251.521069
X-RAY DIFFRACTIONr_mcbond_other1.5251.521068
X-RAY DIFFRACTIONr_mcangle_it2.362.2721359
X-RAY DIFFRACTIONr_mcangle_other2.3592.2721360
X-RAY DIFFRACTIONr_scbond_it1.9051.6731040
X-RAY DIFFRACTIONr_scbond_other1.8841.6691034
X-RAY DIFFRACTIONr_scangle_it2.8552.4431528
X-RAY DIFFRACTIONr_scangle_other2.852.4321514
X-RAY DIFFRACTIONr_lrange_it4.99819.7542475
X-RAY DIFFRACTIONr_lrange_other4.74818.8862352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.3540.3131920.2883859X-RAY DIFFRACTION99.7783
1.391-1.4320.2541520.2423733X-RAY DIFFRACTION99.8971
1.432-1.4760.2561510.2173609X-RAY DIFFRACTION99.7877
1.476-1.5240.2241480.2153459X-RAY DIFFRACTION99.8063
1.524-1.5780.2242010.2033320X-RAY DIFFRACTION99.8865
1.578-1.6370.2311660.1963235X-RAY DIFFRACTION99.7361
1.637-1.7040.2451580.1943100X-RAY DIFFRACTION99.299
1.704-1.780.2191680.1872953X-RAY DIFFRACTION99.4266
1.78-1.8660.2381840.2022797X-RAY DIFFRACTION98.6759
1.866-1.9670.2321100.2042739X-RAY DIFFRACTION99.72
1.967-2.0870.2071250.1992581X-RAY DIFFRACTION99.6318
2.087-2.2310.2281460.2032385X-RAY DIFFRACTION99.1771
2.231-2.4090.2371220.1982283X-RAY DIFFRACTION99.0935
2.409-2.6390.2331030.1862071X-RAY DIFFRACTION99.3148
2.639-2.950.244980.2031909X-RAY DIFFRACTION99.603
2.95-3.4050.275860.2031617X-RAY DIFFRACTION97.9298
3.405-4.1680.198650.1781441X-RAY DIFFRACTION98.3671
4.168-5.8850.297570.231123X-RAY DIFFRACTION99.4941

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