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- PDB-3ce0: Human poly(ADP-ribose) polymerase 3, catalytic fragment in comple... -

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Basic information

Entry
Database: PDB / ID: 3ce0
TitleHuman poly(ADP-ribose) polymerase 3, catalytic fragment in complex with an inhibitor PJ34
ComponentsPoly [ADP-ribose] polymerase 3
KeywordsTRANSFERASE / enzyme-inhibitor complex / catalytic fragment / Structural Genomics / Structural Genomics Consortium / SGC / Alternative splicing / Glycosyltransferase / NAD / Nucleus
Function / homology
Function and homology information


negative regulation of isotype switching / : / NAD+-protein-lysine ADP-ribosyltransferase activity / positive regulation of DNA ligation / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / protein localization to site of double-strand break / protein auto-ADP-ribosylation ...negative regulation of isotype switching / : / NAD+-protein-lysine ADP-ribosyltransferase activity / positive regulation of DNA ligation / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / protein localization to site of double-strand break / protein auto-ADP-ribosylation / intercellular bridge / positive regulation of double-strand break repair via nonhomologous end joining / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / catalytic activity / regulation of mitotic spindle organization / centriole / telomere maintenance / nucleotidyltransferase activity / double-strand break repair / site of double-strand break / nuclear body / centrosome / nucleolus / nucleoplasm / cytoplasm
Similarity search - Function
Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / WGR domain profile. / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain ...Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / WGR domain profile. / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-P34 / Protein mono-ADP-ribosyltransferase PARP3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsLehtio, L. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. ...Lehtio, L. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Welin, M. / Weigelt, J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2009
Title: Structural basis for inhibitor specificity in human poly(ADP-ribose) polymerase-3.
Authors: Lehtio, L. / Jemth, A.S. / Collins, R. / Loseva, O. / Johansson, A. / Markova, N. / Hammarstrom, M. / Flores, A. / Holmberg-Schiavone, L. / Weigelt, J. / Helleday, T. / Schuler, H. / Karlberg, T.
History
DepositionFeb 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0472
Polymers39,7521
Non-polymers2951
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.060, 56.720, 57.040
Angle α, β, γ (deg.)90.000, 112.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly [ADP-ribose] polymerase 3 / PARP-3 / NAD(+) ADP-ribosyltransferase 3 / Poly[ADP-ribose] synthetase 3 / pADPRT-3 / hPARP-3 / IRT1


Mass: 39752.074 Da / Num. of mol.: 1 / Fragment: Catalytic fragment: Residues 178-532
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP3, ADPRT3, ADPRTL3 / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y6F1, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-P34 / N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE


Mass: 295.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N3O2

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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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.9 M DL-Malic acid, 0.1 M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97627 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 30, 2007 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 8249 / Num. obs: 8249 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.74 % / Biso Wilson estimate: 29.72 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 11.11
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.77 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.4 / Num. unique all: 822 / Num. unique obs: 822 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.004data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PA9

2pa9
PDB Unreleased entry


Resolution: 2.8→19.302 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.263 825 10 %RANDOM
Rwork0.207 ---
all0.213 8249 --
obs0.213 8249 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 12.1 Å2 / Biso mean: 38.66 Å2 / Biso min: 179.41 Å2
Baniso -1Baniso -2Baniso -3
1-17.412 Å2-0 Å23.417 Å2
2---12.97 Å2-0 Å2
3----4.443 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2729 0 22 0 2751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022813
X-RAY DIFFRACTIONf_angle_d0.493814
X-RAY DIFFRACTIONf_chiral_restr0.032417
X-RAY DIFFRACTIONf_plane_restr0.002503
X-RAY DIFFRACTIONf_dihedral_angle_d14.3121042
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8-2.9750.3861370.28712351372
2.975-3.2040.3121350.25712131348
3.204-3.5240.2911380.22912471385
3.524-4.030.2111360.18812241360
4.03-5.0620.2081370.15512351372
5.062-19.3030.2521420.1812701412

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