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

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Basic information

Entry
Database: PDB / ID: 7qpw
TitleX-ray structure of the adduct obtained upon reaction of [cis-Rh2(OCOCH3)2(OCOCF3)2] with RNase A (1)
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: 1.15 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 1.1Jan 31, 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 1.2Oct 16, 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)28,6525
Polymers27,4172
Non-polymers1,2363
Water8,809489
1
AAA: 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
BBB: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1022
Polymers13,7081
Non-polymers3941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.500, 32.910, 73.060
Angle α, β, γ (deg.)90.000, 90.164, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-468-

HOH

21BBB-374-

HOH

31BBB-523-

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 / Feature type: SUBJECT OF INVESTIGATION
#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.: 1 / Source method: obtained synthetically / Formula: C4H12O8Rh2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging 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: 1.15→73.06 Å / Num. obs: 84723 / % possible obs: 99.6 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.051 / Net I/σ(I): 10.3
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4212 / CC1/2: 0.738 / Rpim(I) all: 0.479 / % 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: 1.15→73.06 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.228 / SU ML: 0.025 / Cross valid method: FREE R-VALUE / ESU R: 0.034 / ESU R Free: 0.035
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1654 4156 4.892 %
Rwork0.136 80792 -
all0.137 --
obs-84723 99.6 %
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: 17.985 Å2
Baniso -1Baniso -2Baniso -3
1--0.771 Å20 Å20.508 Å2
2--0.268 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.15→73.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 45 489 2415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132169
X-RAY DIFFRACTIONr_bond_other_d0.0030.0181780
X-RAY DIFFRACTIONr_angle_refined_deg3.4041.7042987
X-RAY DIFFRACTIONr_angle_other_deg1.6591.5844205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.345281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.84123.981108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29615365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.199159
X-RAY DIFFRACTIONr_chiral_restr0.110.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022609
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02418
X-RAY DIFFRACTIONr_nbd_refined0.2850.2481
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.21712
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2986
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.2894
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2301
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2060.220
X-RAY DIFFRACTIONr_nbd_other0.230.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.254
X-RAY DIFFRACTIONr_mcbond_it4.2981.551076
X-RAY DIFFRACTIONr_mcbond_other4.31.551075
X-RAY DIFFRACTIONr_mcangle_it4.3152.311373
X-RAY DIFFRACTIONr_mcangle_other4.3132.311374
X-RAY DIFFRACTIONr_scbond_it4.7351.8211093
X-RAY DIFFRACTIONr_scbond_other4.7311.8141087
X-RAY DIFFRACTIONr_scangle_it5.5372.611616
X-RAY DIFFRACTIONr_scangle_other5.5372.5961602
X-RAY DIFFRACTIONr_lrange_it6.31821.792586
X-RAY DIFFRACTIONr_lrange_other5.84119.9492360
X-RAY DIFFRACTIONr_rigid_bond_restr7.57133949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.180.2852760.2465840X-RAY DIFFRACTION97.9343
1.18-1.2120.2572620.2275798X-RAY DIFFRACTION98.6649
1.212-1.2470.2312780.25620X-RAY DIFFRACTION99.983
1.247-1.2860.193030.1835528X-RAY DIFFRACTION100
1.286-1.3280.2022510.1625334X-RAY DIFFRACTION99.9821
1.328-1.3740.1662940.1335069X-RAY DIFFRACTION99.1129
1.374-1.4260.1472820.1164982X-RAY DIFFRACTION99.981
1.426-1.4850.1442630.1094745X-RAY DIFFRACTION99.9601
1.485-1.550.1312520.1054600X-RAY DIFFRACTION100
1.55-1.6260.1492070.1044332X-RAY DIFFRACTION98.8889
1.626-1.7140.1411900.1034235X-RAY DIFFRACTION99.7745
1.714-1.8180.1412090.1053979X-RAY DIFFRACTION99.7618
1.818-1.9430.1681940.1213711X-RAY DIFFRACTION99.6428
1.943-2.0990.1421890.1183462X-RAY DIFFRACTION99.7814
2.099-2.2990.1441590.1233189X-RAY DIFFRACTION98.6737
2.299-2.570.161610.1242888X-RAY DIFFRACTION99.8363
2.57-2.9670.1591390.132562X-RAY DIFFRACTION99.1557
2.967-3.6330.161070.1332196X-RAY DIFFRACTION99.4387
3.633-5.1310.164870.141705X-RAY DIFFRACTION99.8329

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