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- PDB-9ifv: PARP15 catalytic domain mutant (R576E) in complex with 3-aminoben... -

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Basic information

Entry
Database: PDB / ID: 9ifv
TitlePARP15 catalytic domain mutant (R576E) in complex with 3-aminobenzamide
ComponentsProtein mono-ADP-ribosyltransferase PARP15
KeywordsTRANSFERASE / ADP-ribosyltransferase / PARP
Function / homology
Function and homology information


NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression ...NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
: / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like
Similarity search - Domain/homology
3-aminobenzamide / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.431 Å
AuthorsEbenwaldner, C. / Logan, D.T. / Schuler, H. / Moche, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Cancerfonden23-3027Pj Sweden
CitationJournal: Nat Commun / Year: 2025
Title: Regulation of ADP-ribosyltransferase activity by ART domain dimerization in PARP15.
Authors: Ebenwaldner, C. / Garcia Saura, A.G. / Ekstrom, S. / Bernfur, K. / Moche, M. / Logan, D.T. / Cohen, M.S. / Schuler, H.
History
DepositionFeb 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein mono-ADP-ribosyltransferase PARP15
B: Protein mono-ADP-ribosyltransferase PARP15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0954
Polymers50,8232
Non-polymers2722
Water3,909217
1
A: Protein mono-ADP-ribosyltransferase PARP15
hetero molecules

A: Protein mono-ADP-ribosyltransferase PARP15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0954
Polymers50,8232
Non-polymers2722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area1950 Å2
ΔGint-10 kcal/mol
Surface area18970 Å2
MethodPISA
2
B: Protein mono-ADP-ribosyltransferase PARP15
hetero molecules

B: Protein mono-ADP-ribosyltransferase PARP15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0954
Polymers50,8232
Non-polymers2722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area1910 Å2
ΔGint-12 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.713, 76.697, 155.562
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Protein mono-ADP-ribosyltransferase PARP15 / ADP-ribosyltransferase diphtheria toxin-like 7 / ARTD7 / B-aggressive lymphoma protein 3 / Poly ...ADP-ribosyltransferase diphtheria toxin-like 7 / ARTD7 / B-aggressive lymphoma protein 3 / Poly [ADP-ribose] polymerase 15 / PARP-15


Mass: 25411.379 Da / Num. of mol.: 2 / Mutation: R576E
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag and TEV cleavage site / Source: (gene. exp.) Homo sapiens (human) / Gene: PARP15, BAL3 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q460N3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-3AB / 3-aminobenzamide


Mass: 136.151 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C7H8N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M HEPES pH 7.5, 0.02 M MgCl2, 1 mM Spermine-HCl, 5% (w/v) PEG (8K)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.431→77.781 Å / Num. obs: 68482 / % possible obs: 82 % / Redundancy: 12.3 % / Biso Wilson estimate: 24.74 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.032 / Rrim(I) all: 0.116 / Net I/σ(I): 11.2
Reflection shellResolution: 1.431→1.516 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.573 / Num. unique obs: 26535 / % possible all: 26.2

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5084refinement
PHASERphasing
Aimless0.7.9data scaling
autoPROC1.0.5data processing
autoPROC1.0.5data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.431→37.86 Å / SU ML: 0.1986 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.4811
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2252 3397 4.96 %
Rwork0.1967 65050 -
obs0.198 68447 82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.49 Å2
Refinement stepCycle: LAST / Resolution: 1.431→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 0 20 217 3438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01483365
X-RAY DIFFRACTIONf_angle_d1.16974571
X-RAY DIFFRACTIONf_chiral_restr0.0873475
X-RAY DIFFRACTIONf_plane_restr0.0214610
X-RAY DIFFRACTIONf_dihedral_angle_d13.92721259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.431-1.450.363960.268162X-RAY DIFFRACTION1.98
1.45-1.470.4468350.3489540X-RAY DIFFRACTION16.82
1.47-1.50.2781610.30011306X-RAY DIFFRACTION39.03
1.5-1.520.2999810.2691697X-RAY DIFFRACTION52.6
1.52-1.550.30881000.27272002X-RAY DIFFRACTION60.8
1.55-1.580.3011370.25112262X-RAY DIFFRACTION69.56
1.58-1.610.27131420.24512626X-RAY DIFFRACTION80.72
1.61-1.640.29011530.24493007X-RAY DIFFRACTION90.91
1.64-1.670.3031730.28123208X-RAY DIFFRACTION98.46
1.67-1.710.3171930.26443263X-RAY DIFFRACTION99.91
1.71-1.760.2841940.2423197X-RAY DIFFRACTION98.4
1.76-1.80.25611420.23053331X-RAY DIFFRACTION99.97
1.8-1.860.25921780.22553298X-RAY DIFFRACTION99.97
1.86-1.920.2391650.22343068X-RAY DIFFRACTION95.45
1.92-1.980.27931560.22053117X-RAY DIFFRACTION95.51
1.98-2.060.2231420.22333336X-RAY DIFFRACTION100
2.06-2.160.27351680.21113097X-RAY DIFFRACTION93.98
2.16-2.270.26421930.19333090X-RAY DIFFRACTION94.97
2.27-2.410.20141480.1943343X-RAY DIFFRACTION100
2.41-2.60.2322050.19253295X-RAY DIFFRACTION100
2.6-2.860.23471670.19563034X-RAY DIFFRACTION91.2
2.86-3.280.25361600.20243367X-RAY DIFFRACTION100
3.28-4.130.18771250.17552997X-RAY DIFFRACTION87.52
4.13-37.860.16941730.16773507X-RAY DIFFRACTION99.78

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