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- PDB-5na9: The X-ray structure of bovine pancreatic ribonuclease incubated i... -

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Basic information

Entry
Database: PDB / ID: 5na9
TitleThe X-ray structure of bovine pancreatic ribonuclease incubated in the presence of an excess of carboplatin (1:10 ratio)
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / carboplatin / ribonucleases / protein platination
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: 2.07 Å
AuthorsFerraro, G. / Merlino, A.
CitationJournal: J. Inorg. Biochem. / Year: 2017
Title: A comparison study on RNase A oligomerization induced by cisplatin, carboplatin and oxaliplatin.
Authors: Picone, D. / Donnarumma, F. / Ferraro, G. / Gotte, G. / Fagagnini, A. / Butera, G. / Donadelli, M. / Merlino, A.
History
DepositionFeb 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,93015
Polymers13,7081
Non-polymers1,22214
Water3,873215
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-155 kcal/mol
Surface area7150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.168, 64.168, 64.271
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-QPT / carboplatin


Mass: 371.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N2O4Pt / Comment: medication, chemotherapy*YM
#3: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1.5 M ammonium sulfate - 0.1 M sodium acetate pH 5.5 - 3.0 M cesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 22, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.07→55.57 Å / Num. obs: 9665 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 13.6
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RNX

1rnx


Resolution: 2.07→55.57 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.748 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 486 5 %RANDOM
Rwork0.178 ---
obs0.182 9157 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.07→55.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms948 0 17 215 1180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019983
X-RAY DIFFRACTIONr_bond_other_d0.0060.02883
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.931331
X-RAY DIFFRACTIONr_angle_other_deg1.03932043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2455125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42125.22744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86115169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.185154
X-RAY DIFFRACTIONr_chiral_restr0.10.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211138
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02226
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_it1.9011.995500
X-RAY DIFFRACTIONr_mcbond_other1.91.994499
X-RAY DIFFRACTIONr_mcangle_it3.1242.982625
X-RAY DIFFRACTIONr_mcangle_other3.1222.983626
X-RAY DIFFRACTIONr_scbond_it2.5442.234483
X-RAY DIFFRACTIONr_scbond_other2.2452.217478
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7943.218704
X-RAY DIFFRACTIONr_long_range_B_refined7.1918.081276
X-RAY DIFFRACTIONr_long_range_B_other6.39916.8771151
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.12 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 26 -
Rwork0.192 648 -
obs--99.85 %

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