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- PDB-4s18: The X-ray structure of the adduct formed in the reaction between ... -

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Basic information

Entry
Database: PDB / ID: 4s18
TitleThe X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and oxaliplatin
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / ribonuclease fold / cleavage of RNA / RNA / bovine pancreas
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
CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II) / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.27 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 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,2728
Polymers27,4172
Non-polymers1,8566
Water1,18966
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6364
Polymers13,7081
Non-polymers9283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6364
Polymers13,7081
Non-polymers9283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.722, 32.736, 73.233
Angle α, β, γ (deg.)90.00, 90.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-339-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 124 / Label seq-ID: 1 - 124

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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-1PT / CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II) / OXALIPLATIN


Mass: 309.267 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14N2Pt / Comment: medication, antineoplastic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: RNase A was crystallized at room temperature mixing 1 L solution of protein at 20 mg mL-1 with an equal volume of reservoir solution containing 20% PEG4000 and 20 mM sodium citrate buffer pH ...Details: RNase A was crystallized at room temperature mixing 1 L solution of protein at 20 mg mL-1 with an equal volume of reservoir solution containing 20% PEG4000 and 20 mM sodium citrate buffer pH 5.0. Two weeks after their appearance, single crystals were soaked for four days in a solution of Oxaliplatin dissolved in 10 L of reservoir. At the final, Pt drugs:protein concentrations were in 10:1 ratio, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. all: 10764 / Num. obs: 10764 / % possible obs: 95.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.161

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb code 1JVT

1jvt


Resolution: 2.27→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.862 / SU B: 9.639 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.465 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30092 520 4.8 %RANDOM
Rwork0.22451 ---
all0.22825 10237 --
obs0.22825 10237 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.399 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20.76 Å2
2---0.55 Å2-0 Å2
3---1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.27→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 34 66 1935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191918
X-RAY DIFFRACTIONr_bond_other_d0.0040.021749
X-RAY DIFFRACTIONr_angle_refined_deg2.531.9622587
X-RAY DIFFRACTIONr_angle_other_deg1.0834054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6095233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3925.17287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69515327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.413158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0330.0212170
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02434
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_it3.2094.561945
X-RAY DIFFRACTIONr_mcbond_other3.2064.562944
X-RAY DIFFRACTIONr_mcangle_it4.9416.8211173
X-RAY DIFFRACTIONr_mcangle_other4.9396.821174
X-RAY DIFFRACTIONr_scbond_it3.3934.833972
X-RAY DIFFRACTIONr_scbond_other3.3884.832972
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8597.1681416
X-RAY DIFFRACTIONr_long_range_B_refined7.35536.5872232
X-RAY DIFFRACTIONr_long_range_B_other7.34336.6042220
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6193 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.268→2.327 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 33 -
Rwork0.308 629 -
obs--79.28 %

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