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

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Basic information

Entry
Database: PDB / ID: 3fhb
TitleHuman poly(ADP-ribose) polymerase 3, catalytic fragment in complex with an inhibitor 3-aminobenzoic acid
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 / negative regulation of telomerase RNA reverse transcriptase activity / 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 / negative regulation of telomerase RNA reverse transcriptase activity / 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 / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic activity / regulation of mitotic spindle organization / telomere maintenance / centriole / 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
3-AMINOBENZOIC ACID / Protein mono-ADP-ribosyltransferase PARP3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLehtio, L. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Lehtio, L. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Johansson, I. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Schueler, H. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Holmberg-Schiavone, L. / 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
DepositionDec 9, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionJan 6, 2009ID: 2PA9
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,8892
Polymers39,7521
Non-polymers1371
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.240, 56.700, 56.480
Angle α, β, γ (deg.)90.00, 112.86, 90.00
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: UNP residues 178-532
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP3, ADPRT3, ADPRTL3 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y6F1, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-GAB / 3-AMINOBENZOIC ACID / GABACULINE / 3-Aminobenzoic acid


Mass: 137.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 1.8 M DL-Malic acid, 0.1 M Bis-Tris propane - seeding, pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 14, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 14283 / Num. obs: 14283 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 8.73
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.73 / Num. unique all: 1666 / % possible all: 96.3

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Processing

Software
NameVersionClassification
ProDCdata collection
PHASERphasing
REFMAC5.5.0044refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.17 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.884 / SU B: 8.352 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.52 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25379 715 5 %RANDOM
Rwork0.17782 ---
all0.1817 13560 --
obs0.1817 13560 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.759 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.01 Å2
2---0.19 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2766 0 10 144 2920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222840
X-RAY DIFFRACTIONr_bond_other_d0.0010.021908
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9753854
X-RAY DIFFRACTIONr_angle_other_deg0.8734697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6445358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2225.397126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94615484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7881510
X-RAY DIFFRACTIONr_chiral_restr0.0750.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213175
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02509
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_it0.6411.51789
X-RAY DIFFRACTIONr_mcbond_other0.1111.5717
X-RAY DIFFRACTIONr_mcangle_it1.18622887
X-RAY DIFFRACTIONr_scbond_it1.67531051
X-RAY DIFFRACTIONr_scangle_it2.7094.5967
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 51 -
Rwork0.237 956 -
obs--96.73 %

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