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- PDB-4s0q: The X-ray structure of the adduct formed in the reaction between ... -

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Basic information

Entry
Database: PDB / ID: 4s0q
TitleThe X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and carboplatin
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE/RNA / ribonuclease / RNA cleavage / HYDROLASE-RNA complex
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / 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
carboplatin / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsMerlino, A.
CitationJournal: J.Inorg.Biochem. / Year: 2015
Title: Interactions of carboplatin and oxaliplatin with proteins: Insights from X-ray structures and mass spectrometry studies of their ribonuclease A adducts.
Authors: Messori, L. / Marzo, T. / Merlino, A.
History
DepositionJan 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Feb 24, 2016Group: Database references
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1594
Polymers27,4172
Non-polymers7422
Water1,874104
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0802
Polymers13,7081
Non-polymers3711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0802
Polymers13,7081
Non-polymers3711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.521, 32.499, 72.711
Angle α, β, γ (deg.)90.00, 89.59, 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 genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RNASE1, RNS1 / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-QPT / carboplatin


Mass: 371.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12N2O4Pt / Comment: medication, chemotherapy*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Crystals of the RNase A-carboplatin adduct have been obtained by soaking experiments where pre-grown monoclinic protein crystals were incubated with an excess of the platinum drug (at a ...Details: Crystals of the RNase A-carboplatin adduct have been obtained by soaking experiments where pre-grown monoclinic protein crystals were incubated with an excess of the platinum drug (at a protein to platinum ratio 1:10). Crystals of RNase A were grown by hanging-drop vapor mixing 1 L of RNase A at 20 mg mL-1 with equal volumes of reservoir solution containing 20% PEG4000 and 20 mM sodium citrate buffer pH 5.0 at 298 K. Two weeks after their appearance, crystals were soaked for four days in a solution of Carboplatin dissolved in 10 L of reservoir. At the final, Pt drug:protein concentrations were in 10:1 ratio., VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→72.71 Å / Num. all: 14095 / Num. obs: 14095 / % possible obs: 99.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.124

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb code 1JVT, chain A without water molecules and ligands

1jvt


Resolution: 2.09→72.71 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.663 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26175 709 5 %RANDOM
Rwork0.20518 ---
all0.20801 13380 --
obs0.20801 13380 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.837 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-0 Å2-0.16 Å2
2--0.48 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.09→72.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 2 104 1950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191884
X-RAY DIFFRACTIONr_bond_other_d0.0010.021708
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.9262542
X-RAY DIFFRACTIONr_angle_other_deg0.84633948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8955234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51125.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18815330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.612158
X-RAY DIFFRACTIONr_chiral_restr0.1030.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02436
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_it2.7443.631948
X-RAY DIFFRACTIONr_mcbond_other2.7443.631947
X-RAY DIFFRACTIONr_mcangle_it3.9915.4241178
X-RAY DIFFRACTIONr_mcangle_other3.995.4241179
X-RAY DIFFRACTIONr_scbond_it3.2193.916933
X-RAY DIFFRACTIONr_scbond_other3.2193.916933
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6565.7341364
X-RAY DIFFRACTIONr_long_range_B_refined6.46529.1362260
X-RAY DIFFRACTIONr_long_range_B_other6.45429.112233
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.093→2.148 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 55 -
Rwork0.261 909 -
obs--92.16 %

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