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- PDB-4ot4: X-ray Structure of the Adduct formed between cisplatin and Ribonu... -

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Basic information

Entry
Database: PDB / ID: 4ot4
TitleX-ray Structure of the Adduct formed between cisplatin and Ribonuclease A
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / RNase A fold
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
Cisplatin / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMessori, L. / Merlino, A.
CitationJournal: Inorg.Chem. / Year: 2014
Title: Cisplatin binding to proteins: molecular structure of the ribonuclease a adduct.
Authors: Messori, L. / Merlino, A.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Derived calculations
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...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 / struct_conn / struct_site
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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_asym_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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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)28,3175
Polymers27,4172
Non-polymers9003
Water2,252125
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3083
Polymers13,7081
Non-polymers6002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0082
Polymers13,7081
Non-polymers3001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.767, 32.463, 67.575
Angle α, β, γ (deg.)90.00, 93.07, 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 (domestic cattle) / Gene: RNASE1, RNS1 / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.99 Å3/Da / Density % sol: 38.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Crystals of RNase A were grown by hanging-drop vapor diffusion technique at 298 K mixing a protein solution containing 20 mg mL-1 of RNase A with equal volumes of reservoir solution. Well ...Details: Crystals of RNase A were grown by hanging-drop vapor diffusion technique at 298 K mixing a protein solution containing 20 mg mL-1 of RNase A with equal volumes of reservoir solution. Well diffracting crystals appeared within 15days from the following conditions:20% PEG4000 and 20 mM sodium citrate buffer pH 5.0. , 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
DetectorType: RIGAKU SATURN 944+ / Detector: CCD
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 17075 / Num. obs: 17075 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1JVT

1jvt


Resolution: 1.85→30.88 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.675 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.188 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: PHI/PSI TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN PLOT ARE ASSOCIATED WITH RESIDUES THAT ARE NOT WELL DEFINED IN THE ELECTRON DENSITY MAPS (RESIDUES 16-22 OF THE TWO CHAINS AND ...Details: PHI/PSI TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN PLOT ARE ASSOCIATED WITH RESIDUES THAT ARE NOT WELL DEFINED IN THE ELECTRON DENSITY MAPS (RESIDUES 16-22 OF THE TWO CHAINS AND RESIDUES IN CLOSE CONTACT WITH THESE REGIONS).
RfactorNum. reflection% reflectionSelection details
Rfree0.24709 880 5.2 %RANDOM
Rwork0.18924 ---
all0.192 16195 --
obs0.19235 16195 91.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.794 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.24 Å2
2--0.82 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 8 125 1984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191969
X-RAY DIFFRACTIONr_bond_other_d0.0020.021794
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9242670
X-RAY DIFFRACTIONr_angle_other_deg0.9133.0084132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5825253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30925.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06415339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.15158
X-RAY DIFFRACTIONr_chiral_restr0.1150.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02455
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_it2.8132.7581009
X-RAY DIFFRACTIONr_mcbond_other2.8142.7581008
X-RAY DIFFRACTIONr_mcangle_it4.3784.1221263
X-RAY DIFFRACTIONr_mcangle_other4.3764.1221264
X-RAY DIFFRACTIONr_scbond_it2.8022.809958
X-RAY DIFFRACTIONr_scbond_other2.8022.809958
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2354.1391407
X-RAY DIFFRACTIONr_long_range_B_refined8.16121.0562163
X-RAY DIFFRACTIONr_long_range_B_other8.19421.0172129
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.854→1.902 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 60 -
Rwork0.248 978 -
obs--74.78 %

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