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- PDB-5e5f: X-ray structure of the complex between RNase A and compound 4-PF6... -

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Basic information

Entry
Database: PDB / ID: 5e5f
TitleX-ray structure of the complex between RNase A and compound 4-PF6 ([(PPh3)Au(mi-pbi)Pt(Me)(DMSO)][PF6]), the heterobimetallic derivative obtained in the reaction between the organometallic compound [Pt(pbi)(Me)(DMSO)], pbi=2-(2'-pyridil)benzimidazole (compound 3) and the gold(I) compound [Au(Ph3P)][PF6]
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE
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
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.68 Å
AuthorsMerlino, A.
CitationJournal: Dalton Trans / Year: 2015
Title: Cytotoxic properties of a new organometallic platinum(ii) complex and its gold(i) heterobimetallic derivatives.
Authors: Serratrice, M. / Maiore, L. / Zucca, A. / Stoccoro, S. / Landini, I. / Mini, E. / Massai, L. / Ferraro, G. / Merlino, A. / Messori, L. / Cinellu, M.A.
History
DepositionOct 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 2.0Oct 2, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 2.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)27,7695
Polymers27,4172
Non-polymers3523
Water3,351186
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0604
Polymers13,7081
Non-polymers3523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,7081
Polymers13,7081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.487, 31.215, 69.012
Angle α, β, γ (deg.)90.00, 90.69, 90.00
Int Tables number5
Space group name H-MC121

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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, EC: 3.1.27.5
#2: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: RNase A crystals were obtained using the procedure previously described by Vitagliano et al., 200028. Briefly, crystals of the protein were grown by hanging drop vapor diffusion method using ...Details: RNase A crystals were obtained using the procedure previously described by Vitagliano et al., 200028. Briefly, crystals of the protein were grown by hanging drop vapor diffusion method using a reservoir solution containing 22-24 % (w/v) PEG4K, 10 mM sodium citrate pH 5.1-5.3. The crystals are monoclinic, space group C2, with two molecules in the asymmetric unit. The adducts were prepared by a three-days soaking in a solution that comprised the standard mother liquor used for the crystal growth to which a 2.5-5 mM solution of each compound was added. Crystal soaked in this solution were mounted for the X-ray data collection without using a cryoprotectant, as done in previous studies30.
PH range: 5.1-5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→69 Å / Num. obs: 23228 / % possible obs: 95 % / Redundancy: 2.4 % / Net I/σ(I): 6.5
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 2 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.68→69 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.153 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23404 1188 5.1 %RANDOM
Rwork0.18332 ---
obs0.18601 22040 94.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.167 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.17 Å2
2--0.33 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.68→69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 10 186 2094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191973
X-RAY DIFFRACTIONr_bond_other_d0.0020.021765
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.9252676
X-RAY DIFFRACTIONr_angle_other_deg0.88334084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8485252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9325.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13415335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.81158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022304
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5262.8331006
X-RAY DIFFRACTIONr_mcbond_other2.5152.8311004
X-RAY DIFFRACTIONr_mcangle_it3.3544.2371258
X-RAY DIFFRACTIONr_mcangle_other3.3534.241259
X-RAY DIFFRACTIONr_scbond_it3.283.084967
X-RAY DIFFRACTIONr_scbond_other3.2793.083968
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7844.4941419
X-RAY DIFFRACTIONr_long_range_B_refined6.54422.912270
X-RAY DIFFRACTIONr_long_range_B_other6.56222.8952268
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.682→1.726 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 77 -
Rwork0.277 1449 -
obs--84.73 %

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