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- PDB-6gok: X-ray structure of the adduct formed upon reaction of bovine panc... -

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Basic information

Entry
Database: PDB / ID: 6gok
TitleX-ray structure of the adduct formed upon reaction of bovine pancreatic ribonuclease with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / protein-metallodrug interaction / palladium-based drug / N-pyridylbenzimidazole bidentate ligands / stacking / non covalent bond
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
N,N-pyridylbenzimidazole derivative-Pd complex / PALLADIUM ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMerlino, A. / Ferraro, G.
CitationJournal: Dalton Trans / Year: 2018
Title: Exploring the interactions between model proteins and Pd(ii) or Pt(ii) compounds bearing charged N,N-pyridylbenzimidazole bidentate ligands by X-ray crystallography.
Authors: Ferraro, G. / Mansour, A.M. / Merlino, A.
History
DepositionJun 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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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)28,6196
Polymers27,4172
Non-polymers1,2024
Water1,13563
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3093
Polymers13,7081
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3093
Polymers13,7081
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.282, 32.805, 72.661
Angle α, β, γ (deg.)90.00, 90.61, 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 natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-PD / PALLADIUM ION


Mass: 106.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pd
#3: Chemical ChemComp-F6Q / N,N-pyridylbenzimidazole derivative-Pd complex


Mass: 494.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15Cl2N3O3PdS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 20% PEG4000 10 mM sodium citrate buffer pH 5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→72.66 Å / Num. obs: 6649 / % possible obs: 91.1 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 286 / CC1/2: 0.834 / % possible all: 79.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fs3

1fs3


Resolution: 2.65→72.66 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.889 / SU B: 14.123 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25476 309 4.8 %RANDOM
Rwork0.18722 ---
obs0.19066 6196 91.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.959 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0 Å21.35 Å2
2--1.43 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 2.65→72.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 49 63 2014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191999
X-RAY DIFFRACTIONr_bond_other_d0.0050.021704
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9692715
X-RAY DIFFRACTIONr_angle_other_deg1.2053.0054001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0875248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10425.28189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51515337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.549158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212228
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021382
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_it3.3014.996995
X-RAY DIFFRACTIONr_mcbond_other3.3014.996994
X-RAY DIFFRACTIONr_mcangle_it5.2877.4821243
X-RAY DIFFRACTIONr_mcangle_other5.2867.4831243
X-RAY DIFFRACTIONr_scbond_it3.0875.1111004
X-RAY DIFFRACTIONr_scbond_other3.0865.1111005
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0627.5331484
X-RAY DIFFRACTIONr_long_range_B_refined8.04555.8192301
X-RAY DIFFRACTIONr_long_range_B_other8.04355.8092302
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 13 -
Rwork0.273 406 -
obs--81.04 %

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