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- PDB-32hb: PARP9 Macro Domain 2 P347G mutant, Free form -

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Basic information

Entry
Database: PDB / ID: 32hb
TitlePARP9 Macro Domain 2 P347G mutant, Free form
ComponentsProtein mono-ADP-ribosyltransferase PARP9
KeywordsHYDROLASE / PARP9 / ADPR / macro domain
Function / homology
Function and homology information


regulation of response to type II interferon / NAD+-protein-C-terminal glycine ADP-ribosyltransferase activity / positive regulation of type II interferon-mediated signaling pathway / ADP-D-ribose binding / negative regulation of catalytic activity / nicotinate metabolic process / positive regulation of chromatin binding / Maturation of nucleoprotein / Nicotinate metabolism / Maturation of nucleoprotein ...regulation of response to type II interferon / NAD+-protein-C-terminal glycine ADP-ribosyltransferase activity / positive regulation of type II interferon-mediated signaling pathway / ADP-D-ribose binding / negative regulation of catalytic activity / nicotinate metabolic process / positive regulation of chromatin binding / Maturation of nucleoprotein / Nicotinate metabolism / Maturation of nucleoprotein / post-transcriptional regulation of gene expression / STAT family protein binding / positive regulation of tyrosine phosphorylation of STAT protein / Transferases; Glycosyltransferases; Pentosyltransferases / ubiquitin-like protein ligase binding / NAD+ poly-ADP-ribosyltransferase activity / DNA damage checkpoint signaling / positive regulation of defense response to virus by host / nucleotidyltransferase activity / enzyme inhibitor activity / site of DNA damage / positive regulation of protein localization to nucleus / double-strand break repair / transcription corepressor activity / cell migration / histone binding / defense response to virus / viral protein processing / negative regulation of gene expression / innate immune response / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / PARP14-like, eighth type I KH 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
NITRATE ION / Protein mono-ADP-ribosyltransferase PARP9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChikunova, A. / Fourkiotis, K.N. / Spyroulias, A.G. / Perrakis, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)101087215-ESPERANCEEuropean Union
CitationJournal: To Be Published
Title: So different, yet so similar: the paradigm of PARP9 macro domain paralogs
Authors: Fourkiotis, K.N. / Sideras-Bisdekis, C. / Tsika, C.A. / Fish, A. / Kravvariti, P.K. / Tsatsouli, S.A. / Perrakis, A. / Chikunova, A. / Spyroulias, A.G.
History
DepositionJul 9, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein mono-ADP-ribosyltransferase PARP9
B: Protein mono-ADP-ribosyltransferase PARP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9006
Polymers44,3862
Non-polymers5144
Water1,54986
1
A: Protein mono-ADP-ribosyltransferase PARP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4503
Polymers22,1931
Non-polymers2572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein mono-ADP-ribosyltransferase PARP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4503
Polymers22,1931
Non-polymers2572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.988, 73.917, 58.432
Angle α, β, γ (deg.)90.00, 117.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein mono-ADP-ribosyltransferase PARP9 / ADP-ribosyltransferase diphtheria toxin-like 9 / ARTD9 / B aggressive lymphoma protein / Poly [ADP- ...ADP-ribosyltransferase diphtheria toxin-like 9 / ARTD9 / B aggressive lymphoma protein / Poly [ADP-ribose] polymerase 9 / PARP-9


Mass: 22192.803 Da / Num. of mol.: 2 / Mutation: P347G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP9, BAL, BAL1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8IXQ6, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.34 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M NPS, 0.1 M Imidazole/MES buffer, 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.9→73.92 Å / Num. obs: 32263 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 2059 / CC1/2: 0.746

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→52 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 8.465 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21754 1628 5 %RANDOM
Rwork0.18435 ---
obs0.18603 30613 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.263 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å2-0.48 Å2
2---2.26 Å20 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 1.9→52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 32 86 3011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122987
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162928
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.8164034
X-RAY DIFFRACTIONr_angle_other_deg0.5561.7546767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5375363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.02652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62710555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02624
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_it2.392.8071461
X-RAY DIFFRACTIONr_mcbond_other2.3882.8061461
X-RAY DIFFRACTIONr_mcangle_it3.4445.0181821
X-RAY DIFFRACTIONr_mcangle_other3.4435.0181822
X-RAY DIFFRACTIONr_scbond_it4.0133.3911526
X-RAY DIFFRACTIONr_scbond_other3.9913.3891524
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9235.9812214
X-RAY DIFFRACTIONr_long_range_B_refined7.35527.33158
X-RAY DIFFRACTIONr_long_range_B_other7.35427.313159
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 126 -
Rwork0.298 2249 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4117-0.0858-0.46383.1974-0.88322.6906-0.0004-0.0922-0.2077-0.0239-0.0719-0.15420.26340.16280.07230.05580.02630.00010.01720.01120.026114.9457-0.472315.5022
22.9139-0.93690.26874.013-0.87232.55260.00250.16140.2228-0.0257-0.0653-0.2431-0.12580.11520.06280.0195-0.0109-00.01570.01370.02519.358325.03675.153
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A310 - 494
2X-RAY DIFFRACTION2B309 - 497

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