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- PDB-5obe: X-ray structure of the adduct formed upon reaction of ribonucleas... -

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Basic information

Entry
Database: PDB / ID: 5obe
TitleX-ray structure of the adduct formed upon reaction of ribonuclease A with the compound fac-[RuII(CO)3Cl2(N3-MBI), MBI=methyl-benzimidazole
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / protein-metallodrug interaction / CO releasing molecules
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
Chem-9Q8 / PHOSPHATE ION / Chem-RU2 / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsPontillo, N. / Ferraro, G. / Merlino, A.
CitationJournal: Dalton Trans / Year: 2017
Title: Ru-Based CO releasing molecules with azole ligands: interaction with proteins and the CO release mechanism disclosed by X-ray crystallography.
Authors: Pontillo, N. / Ferraro, G. / Messori, L. / Tamasi, G. / Merlino, A.
History
DepositionJun 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 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)28,0626
Polymers27,4172
Non-polymers6454
Water7,494416
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1174
Polymers13,7081
Non-polymers4093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9442
Polymers13,7081
Non-polymers2361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.651, 32.983, 73.046
Angle α, β, γ (deg.)90.00, 90.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-416-

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-RU2 / pentakis(oxidaniumyl)-(oxidaniumylidynemethyl)ruthenium


Mass: 219.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH10O6Ru
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-9Q8 / tris(oxidaniumylidynemethyl)-tris(oxidanyl)ruthenium


Mass: 236.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H3O6Ru
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 22% PEG4K, 10 mM sodium citrate pH 5.1 Soaking: 3 days Ligand con-centration: 5 mM

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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 / Date: Oct 6, 2014 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.82→73.05 Å / Num. obs: 21285 / % possible obs: 97.6 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 6.3
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 1.7 / % possible all: 95.4

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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: 1JVT mol A

1jvt


Resolution: 1.82→73.05 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.253 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23577 1091 5.1 %RANDOM
Rwork0.16546 ---
obs0.16896 20184 95.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å2-0.52 Å2
2---0.11 Å2-0 Å2
3---0.6 Å2
Refinement stepCycle: 1 / Resolution: 1.82→73.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 23 416 2341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022044
X-RAY DIFFRACTIONr_bond_other_d0.0020.021847
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9382772
X-RAY DIFFRACTIONr_angle_other_deg1.01634288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2665266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32225.16193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68715363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.169159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022355
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02472
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_it2.7712.911022
X-RAY DIFFRACTIONr_mcbond_other2.7662.911021
X-RAY DIFFRACTIONr_mcangle_it4.2144.3551284
X-RAY DIFFRACTIONr_mcangle_other4.2134.3561285
X-RAY DIFFRACTIONr_scbond_it2.8483.0531022
X-RAY DIFFRACTIONr_scbond_other2.6613.021003
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0984.4311457
X-RAY DIFFRACTIONr_long_range_B_refined8.76624.8242664
X-RAY DIFFRACTIONr_long_range_B_other8.45123.6622418
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.808→1.855 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 52 -
Rwork0.281 956 -
obs--62.18 %

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