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- PDB-6f60: The x-ray structure of bovine pancreatic ribonuclease in complex ... -

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Basic information

Entry
Database: PDB / ID: 6f60
TitleThe x-ray structure of bovine pancreatic ribonuclease in complex with a five-coordinate platinum(II) compound containing a sugar ligand
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / ribonuclease / platinum(II) compound / five-coordinate / sugar ligand / cytotoxicity
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
five-coordinate platinum(II) compound / five-coordinate platinum(II) compound / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.14 Å
AuthorsMerlino, A. / Ferraro, G.
CitationJournal: Inorg Chem / Year: 2018
Title: Five-Coordinate Platinum(II) Compounds Containing Sugar Ligands: Synthesis, Characterization, Cytotoxic Activity, and Interaction with Biological Macromolecules.
Authors: Cucciolito, M.E. / D'Amora, A. / De Feo, G. / Ferraro, G. / Giorgio, A. / Petruk, G. / Monti, D.M. / Merlino, A. / Ruffo, F.
History
DepositionDec 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms
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)28,6845
Polymers27,4172
Non-polymers1,2673
Water9,728540
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-18 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.780, 32.519, 72.337
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

21B-538-

HOH

31B-560-

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, EC: 3.1.27.5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DVW / five-coordinate platinum(II) compound


Mass: 728.657 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31N7O5Pt
#4: Chemical ChemComp-DW5 / five-coordinate platinum(II) compound


Mass: 442.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N2Pt
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 4K 0.01 M sodium citrate pH 5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.14→72.34 Å / Num. obs: 80973 / % possible obs: 95.5 % / Redundancy: 2.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.034 / Net I/σ(I): 8.7
Reflection shellResolution: 1.14→1.18 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 0.9 / CC1/2: 0.363 / Rpim(I) all: 0.805 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.14→72.34 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.209 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.044 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 4171 5.2 %RANDOM
Rwork0.13826 ---
obs0.14123 76770 95.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.744 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å21.37 Å2
2---1.59 Å2-0 Å2
3---2.46 Å2
Refinement stepCycle: 1 / Resolution: 1.14→72.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 52 540 2494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0192268
X-RAY DIFFRACTIONr_bond_other_d0.0030.021921
X-RAY DIFFRACTIONr_angle_refined_deg2.5341.9423098
X-RAY DIFFRACTIONr_angle_other_deg1.8473.0024536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9365302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84825.392102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40615398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.439159
X-RAY DIFFRACTIONr_chiral_restr0.1530.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022675
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02446
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_it6.8532.2271133
X-RAY DIFFRACTIONr_mcbond_other6.8562.2261132
X-RAY DIFFRACTIONr_mcangle_it7.9713.3651460
X-RAY DIFFRACTIONr_mcangle_other7.9683.3651461
X-RAY DIFFRACTIONr_scbond_it5.492.5681135
X-RAY DIFFRACTIONr_scbond_other5.5111136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.09414.3831639
X-RAY DIFFRACTIONr_long_range_B_refined11.14832.7592973
X-RAY DIFFRACTIONr_long_range_B_other11.14832.7582973
X-RAY DIFFRACTIONr_rigid_bond_restr6.26534185
X-RAY DIFFRACTIONr_sphericity_free39.975271
X-RAY DIFFRACTIONr_sphericity_bonded24.24854419
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 298 -
Rwork0.335 5421 -
obs--91.56 %

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