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- PDB-8oo3: X-ray structure of the adduct formed upon reaction of cisplatin w... -

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Basic information

Entry
Database: PDB / ID: 8oo3
TitleX-ray structure of the adduct formed upon reaction of cisplatin with human angiogenin after 5 days soaking
ComponentsAngiogenin
KeywordsHYDROLASE / angiogenin / CDDP / ROS production / prostate cancer
Function / homology
Function and homology information


activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / rRNA transcription / basement membrane / RNA nuclease activity / positive regulation of endothelial cell proliferation / actin filament polymerization / positive regulation of protein secretion ...activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / rRNA transcription / basement membrane / RNA nuclease activity / positive regulation of endothelial cell proliferation / actin filament polymerization / positive regulation of protein secretion / negative regulation of smooth muscle cell proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / heparin binding / actin binding / cytoplasmic vesicle / angiogenesis / endonuclease activity / negative regulation of translation / cell differentiation / response to hypoxia / defense response to Gram-positive bacterium / copper ion binding / innate immune response / signaling receptor binding / nucleolus / protein homodimerization activity / DNA binding / extracellular space / nucleus
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
AMMONIA / : / D(-)-TARTARIC ACID / Angiogenin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsFerraro, G. / Merlino, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Dalton Trans / Year: 2023
Title: Cisplatin binding to angiogenin protein: new molecular pathways and targets for the drug's anticancer activity.
Authors: Ferraro, G. / Sanfilippo, V. / Chiaverini, L. / Satriano, C. / Marzo, T. / Merlino, A. / La Mendola, D.
History
DepositionApr 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6235
Polymers14,1691
Non-polymers4544
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.320, 37.480, 38.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11AAA-331-

HOH

21AAA-393-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Angiogenin / Ribonuclease 5 / RNase 5


Mass: 14169.036 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANG, RNASE5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q71MJ0, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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Non-polymers , 5 types, 98 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NH3 / AMMONIA


Mass: 17.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH3
#4: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 10% PEG6K, 20 mM sodium citrate pH 5.1, 0.2 M sodium/potassium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→42.66 Å / Num. obs: 12229 / % possible obs: 95 % / Redundancy: 10.7 % / CC1/2: 1 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.1
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 535 / CC1/2: 0.856 / % possible all: 83.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→42.66 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.855 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.212 / SU B: 4.086 / SU ML: 0.132 / Average fsc free: 0.7958 / Average fsc work: 0.8048 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.166
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2905 619 5.11 %
Rwork0.243 11495 -
all0.245 --
obs-12114 94.893 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.824 Å2
Baniso -1Baniso -2Baniso -3
1--0.149 Å2-0 Å2-0 Å2
2---0.049 Å20 Å2
3---0.198 Å2
Refinement stepCycle: LAST / Resolution: 1.76→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 18 94 1097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131055
X-RAY DIFFRACTIONr_bond_other_d0.0020.017936
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.6741426
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5922180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.045128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.6062068
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08815181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4031513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021199
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02244
X-RAY DIFFRACTIONr_nbd_refined0.1910.2184
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.2870
X-RAY DIFFRACTIONr_nbtor_refined0.1590.2485
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2485
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.257
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1640.215
X-RAY DIFFRACTIONr_nbd_other0.2320.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2590.214
X-RAY DIFFRACTIONr_mcbond_it2.1771.961503
X-RAY DIFFRACTIONr_mcbond_other2.1511.951502
X-RAY DIFFRACTIONr_mcangle_it3.462.926631
X-RAY DIFFRACTIONr_mcangle_other3.4642.936632
X-RAY DIFFRACTIONr_scbond_it2.5772.339552
X-RAY DIFFRACTIONr_scbond_other2.5612.334549
X-RAY DIFFRACTIONr_scangle_it4.0933.356794
X-RAY DIFFRACTIONr_scangle_other4.0923.354793
X-RAY DIFFRACTIONr_lrange_it6.53523.641124
X-RAY DIFFRACTIONr_lrange_other6.5223.5291120
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.76-1.8060.299410.2187160.2239220.9030.93482.10410.215
1.806-1.8550.266350.2938090.2919060.7210.60393.15670.271
1.855-1.9090.467400.4076870.418730.4560.40883.27610.375
1.909-1.9670.563340.5546860.5548370.4160.41786.02150.513
1.967-2.0320.268340.2528000.2538340.7590.811000.22
2.032-2.1030.252630.2467370.2468000.8320.8411000.218
2.103-2.1820.244460.257190.2497660.6680.71699.86950.223
2.182-2.2710.472260.4455970.4467490.6990.70383.17760.387
2.271-2.3720.4390.2896440.2957130.7440.81995.79240.254
2.372-2.4870.225240.2026610.2036850.9150.9191000.177
2.487-2.6210.309390.1926260.1996650.8990.9291000.171
2.621-2.7790.278250.2065960.2096210.9050.9261000.186
2.779-2.970.242280.1955720.1986000.9190.9321000.182
2.97-3.2070.334270.25230.2065500.8890.9381000.194
3.207-3.5110.21270.1824860.1845130.9550.9561000.181
3.511-3.9220.22260.1744390.1764660.9470.96499.78540.172
3.922-4.5230.204250.1623890.1644160.9590.9799.51920.179
4.523-5.5230.26200.1743500.1793700.9580.9681000.198
5.523-7.7470.212130.2362810.2352940.9670.9371000.259
7.747-42.660.32870.2341720.2381810.9060.94798.8950.255

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