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

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Basic information

Entry
Database: PDB / ID: 7qpy
TitleX-ray structure of the adduct obtained upon reaction of [cis-Rh2(OCOCH3)2(OCOCF3)2] with RNase A (3)
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) / Chem-F5I / Chem-F5T / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 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
Revision 1.2Nov 20, 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
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0466
Polymers27,4172
Non-polymers1,6304
Water5,981332
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5503
Polymers13,7081
Non-polymers8422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4963
Polymers13,7081
Non-polymers7882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.220, 32.500, 72.380
Angle α, β, γ (deg.)90.000, 90.408, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-403-

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-F5T / cis-bis(mi2-acetato-O, O')-(mi2-trifluoroacetato-O, O')-diaquo-dirhodium (II)


Mass: 473.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11F3O8Rh2
#3: Chemical ChemComp-F3I / (mi2-acetato-O, O')-hexaaquo-dirhodium (II)


Mass: 367.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H10O8Rh2
#4: Chemical ChemComp-F5I / cis-bis(mi2-acetato-O, O')-tetraaquo-dirhodium(II)


Mass: 393.944 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H12O8Rh2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.1 / Details: 22 % PEG 4K 0.01 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: May 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→50.115 Å / Num. obs: 44454 / % possible obs: 99.1 % / Redundancy: 6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.05 / Net I/σ(I): 12.7
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2037 / CC1/2: 0.79 / Rpim(I) all: 0.406 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: !JVT

Resolution: 1.42→50.115 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.194 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2122 2314 5.239 %
Rwork0.1767 41857 -
all0.179 --
obs-44171 99.192 %
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: 20.709 Å2
Baniso -1Baniso -2Baniso -3
1--0.026 Å20 Å20.066 Å2
2---0.005 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.42→50.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 55 333 2266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132075
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151771
X-RAY DIFFRACTIONr_angle_refined_deg3.691.7162859
X-RAY DIFFRACTIONr_angle_other_deg1.541.5884110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1585262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50424.158101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55915343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.123158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022526
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02463
X-RAY DIFFRACTIONr_nbd_refined0.2010.2460
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21751
X-RAY DIFFRACTIONr_nbtor_refined0.170.2993
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2236
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.217
X-RAY DIFFRACTIONr_nbd_other0.180.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0660.21
X-RAY DIFFRACTIONr_mcbond_it2.1961.9651024
X-RAY DIFFRACTIONr_mcbond_other2.1961.9651023
X-RAY DIFFRACTIONr_mcangle_it3.4142.9381291
X-RAY DIFFRACTIONr_mcangle_other3.4132.9381292
X-RAY DIFFRACTIONr_scbond_it2.6862.2041051
X-RAY DIFFRACTIONr_scbond_other2.6782.1971045
X-RAY DIFFRACTIONr_scangle_it4.1123.2191567
X-RAY DIFFRACTIONr_scangle_other4.0183.2041553
X-RAY DIFFRACTIONr_lrange_it6.81325.3732454
X-RAY DIFFRACTIONr_lrange_other6.81625.0142417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.4570.2961370.2412955X-RAY DIFFRACTION94.934
1.457-1.4970.2461490.2192988X-RAY DIFFRACTION98.2769
1.497-1.540.2891670.2152891X-RAY DIFFRACTION99.3502
1.54-1.5870.2282040.1952771X-RAY DIFFRACTION99.5316
1.587-1.6390.2251480.1952759X-RAY DIFFRACTION99.4867
1.639-1.6970.2331210.182707X-RAY DIFFRACTION99.6476
1.697-1.7610.2371380.1772576X-RAY DIFFRACTION99.8528
1.761-1.8330.1781300.1712479X-RAY DIFFRACTION99.8851
1.833-1.9140.2261220.1822391X-RAY DIFFRACTION99.446
1.914-2.0070.211350.1742271X-RAY DIFFRACTION99.834
2.007-2.1160.2371310.1742165X-RAY DIFFRACTION99.913
2.116-2.2440.221080.1852062X-RAY DIFFRACTION99.816
2.244-2.3980.21200.1761939X-RAY DIFFRACTION99.6612
2.398-2.590.211040.1641794X-RAY DIFFRACTION99.8947
2.59-2.8370.194980.1691654X-RAY DIFFRACTION99.7154
2.837-3.170.215770.1781539X-RAY DIFFRACTION99.8147
3.17-3.6580.177730.1471349X-RAY DIFFRACTION99.6496
3.658-4.4740.187540.1581150X-RAY DIFFRACTION99.6689
4.474-6.3030.183670.166886X-RAY DIFFRACTION99.0645

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