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- PDB-6qe9: The X-ray structure of the adduct formed in the reaction between ... -

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Basic information

Entry
Database: PDB / ID: 6qe9
TitleThe X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and complex I, a pentacoordinate Pt(II) compound containing 2,9-dimethyl-1,10-phenanthroline, dimethylfumarate, methyl and iodine as ligands
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / five-coordinate Pt complexes / anticancer platinum compounds / protein metal coordination
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
pentacoordinate Pt(II) compound / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsMerlino, A. / Ferraro, G.
CitationJournal: Int J Mol Sci / Year: 2019
Title: Reaction with Proteins of a Five-Coordinate Platinum(II) Compound.
Authors: Ferraro, G. / Marzo, T. / Cucciolito, M.E. / Ruffo, F. / Messori, L. / Merlino, A.
History
DepositionJan 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.2Nov 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)28,4325
Polymers27,4172
Non-polymers1,0153
Water2,576143
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2643
Polymers13,7081
Non-polymers5552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1682
Polymers13,7081
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.005, 30.655, 68.680
Angle α, β, γ (deg.)90.00, 92.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-363-

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-J9H / pentacoordinate Pt(II) compound


Mass: 459.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N3Pt
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 1.9 Å3/Da / Density % sol: 35.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG4K 0.01 M sodium citrate pH 5.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 12949 / % possible obs: 94.8 % / Redundancy: 2.8 % / Biso Wilson estimate: 30.08 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.9
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.3 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JVT

1jvt


Resolution: 2.03→22.89 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.811 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25423 636 4.9 %RANDOM
Rwork0.17653 ---
obs0.18016 12313 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.826 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20.47 Å2
2--1.12 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.03→22.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 29 143 2068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131983
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181689
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.6672690
X-RAY DIFFRACTIONr_angle_other_deg1.3341.5853960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3465252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39324.02197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05815334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.479158
X-RAY DIFFRACTIONr_chiral_restr0.0650.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022264
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02384
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_it2.4333.2221005
X-RAY DIFFRACTIONr_mcbond_other2.4323.2211004
X-RAY DIFFRACTIONr_mcangle_it3.7194.8241258
X-RAY DIFFRACTIONr_mcangle_other3.7184.8251259
X-RAY DIFFRACTIONr_scbond_it2.6733.446978
X-RAY DIFFRACTIONr_scbond_other2.6723.444979
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1985.0671435
X-RAY DIFFRACTIONr_long_range_B_refined6.62738.672277
X-RAY DIFFRACTIONr_long_range_B_other6.6438.6732278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.031→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 56 -
Rwork0.24 858 -
obs--91.04 %

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