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- PDB-9qyd: PARP9 Macro domain 1, Free form -

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Basic information

Entry
Database: PDB / ID: 9qyd
TitlePARP9 Macro domain 1, Free form
ComponentsProtein mono-ADP-ribosyltransferase PARP9
KeywordsHYDROLASE / Macro domain / Free Form / PARP9
Function / homology
Function and homology information


regulation of response to type II interferon / NAD+-protein-C-terminal glycine ADP-ribosyltransferase activity / ADP-D-ribose binding / positive regulation of type II interferon-mediated signaling pathway / negative regulation of catalytic activity / : / : / Maturation of nucleoprotein / positive regulation of chromatin binding / Maturation of nucleoprotein ...regulation of response to type II interferon / NAD+-protein-C-terminal glycine ADP-ribosyltransferase activity / ADP-D-ribose binding / positive regulation of type II interferon-mediated signaling pathway / negative regulation of catalytic activity / : / : / Maturation of nucleoprotein / positive regulation of chromatin binding / Maturation of nucleoprotein / positive regulation of tyrosine phosphorylation of STAT protein / STAT family protein binding / post-transcriptional regulation of gene expression / ubiquitin-like protein ligase binding / enzyme inhibitor activity / site of DNA damage / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of defense response to virus by host / nucleotidyltransferase activity / DNA damage checkpoint signaling / positive regulation of protein localization to nucleus / transcription corepressor activity / cell migration / double-strand break repair / defense response to virus / histone binding / viral protein processing / innate immune response / negative regulation of gene expression / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / membrane / 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
MALONATE ION / Protein mono-ADP-ribosyltransferase PARP9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsFourkiotis, N.K. / Chikunova, A. / Tsika, C.A. / Tsatsouli, A.S. / Perrakis, A. / Spyroulias, G.A.
Funding supportEuropean Union, 4items
OrganizationGrant numberCountry
European Regional Development Fund5002550-INSPIREDEuropean Union
European Union (EU)101087215-ESPERANCEEuropean Union
European Union (EU)101159708-MILESTONEEuropean Union
European Union (EU)101159708-iNEXT DiscoveryEuropean Union
CitationJournal: To Be Published
Title: Comparative analysis of hPARP9 macro domains
Authors: Fourkiotis, N.K. / Chikunova, A. / Tsika, C.A. / Tsatsouli, A.S. / Perrakis, A. / Spyroulias, G.A.
History
DepositionApr 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,3915
Polymers22,0031
Non-polymers3884
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint5 kcal/mol
Surface area9240 Å2
Unit cell
Length a, b, c (Å)39.701, 63.847, 69.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2122
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21A-524-

HOH

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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: 22002.564 Da / Num. of mol.: 1
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4M Sodium malonate, 4% PPG P400

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.91→47.03 Å / Num. obs: 14316 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.998 / Net I/σ(I): 9.4
Reflection shellResolution: 1.91→1.96 Å / Num. unique obs: 946 / CC1/2: 0.535 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDS4.4.7data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→47.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.082 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23507 753 5.3 %RANDOM
Rwork0.18679 ---
obs0.18931 13536 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.821 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0 Å2-0 Å2
2--0.27 Å2-0 Å2
3---0.66 Å2
Refinement stepCycle: 1 / Resolution: 1.91→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 26 70 1592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121590
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161572
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.8122155
X-RAY DIFFRACTIONr_angle_other_deg0.5231.753620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9975204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.58157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40610282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
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_it2.2332.757804
X-RAY DIFFRACTIONr_mcbond_other2.2312.757804
X-RAY DIFFRACTIONr_mcangle_it3.2844.9441012
X-RAY DIFFRACTIONr_mcangle_other3.2834.9441013
X-RAY DIFFRACTIONr_scbond_it3.5243.293786
X-RAY DIFFRACTIONr_scbond_other3.5223.295787
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3945.8011144
X-RAY DIFFRACTIONr_long_range_B_refined7.53730.581739
X-RAY DIFFRACTIONr_long_range_B_other7.50929.741726
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 56 -
Rwork0.298 983 -
obs--100 %

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