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- PDB-3gey: Crystal structure of human poly(ADP-ribose) polymerase 15, cataly... -

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Basic information

Entry
Database: PDB / ID: 3gey
TitleCrystal structure of human poly(ADP-ribose) polymerase 15, catalytic fragment in complex with an inhibitor Pj34
ComponentsPoly [ADP-ribose] polymerase 15
KeywordsTRANSFERASE / PARP / POLY(ADP-RIBOSE) POLYMERASE / BAL-3 / SGC / STRUCTURAL GENOMICS CONSORTIUM / Glycosyltransferase / NAD / Nucleus / Transcription / Transcription regulation
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
: / 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. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain ...: / 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. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-P34 / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKarlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Karlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Schutz, P. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Lack of ADP-ribosyltransferase Activity in Poly(ADP-ribose) Polymerase-13/Zinc Finger Antiviral Protein.
Authors: Karlberg, T. / Klepsch, M. / Thorsell, A.G. / Andersson, C.D. / Linusson, A. / Schuler, H.
History
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Apr 22, 2015Group: Database references
Revision 1.4Sep 6, 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
Revision 1.5May 29, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 15
B: Poly [ADP-ribose] polymerase 15
C: Poly [ADP-ribose] polymerase 15
D: Poly [ADP-ribose] polymerase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3496
Polymers101,7584
Non-polymers5912
Water48627
1
A: Poly [ADP-ribose] polymerase 15
D: Poly [ADP-ribose] polymerase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1743
Polymers50,8792
Non-polymers2951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-14 kcal/mol
Surface area18290 Å2
MethodPISA
2
B: Poly [ADP-ribose] polymerase 15
C: Poly [ADP-ribose] polymerase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1743
Polymers50,8792
Non-polymers2951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-16 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.080, 137.630, 68.050
Angle α, β, γ (deg.)90.00, 90.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Poly [ADP-ribose] polymerase 15 / PARP-15 / B-aggressive lymphoma protein 3


Mass: 25439.459 Da / Num. of mol.: 4 / Fragment: Catalytic domain: Residues 459-656
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAL3, PARP15 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q460N3, 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.: 2 / Source method: obtained synthetically / Formula: C17H17N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 26% PEG 3350, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98004 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Dec 10, 2008
Details: Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focusing
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98004 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 42012 / Num. obs: 42012 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.102 / Rsym value: 0.097 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 5.7 / Rsym value: 0.256 / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BLJ

3blj


Resolution: 2.2→24.193 Å / σ(F): 1.99 / Phase error: 38.48 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2697 2016 4.83 %
Rwork0.2118 --
obs0.2118 41728 99.4 %
all-41728 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.866 Å2 / ksol: 0.397 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→24.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6224 0 44 27 6295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056440
X-RAY DIFFRACTIONf_angle_d0.8098734
X-RAY DIFFRACTIONf_dihedral_angle_d16.552305
X-RAY DIFFRACTIONf_chiral_restr0.055912
X-RAY DIFFRACTIONf_plane_restr0.0031138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23790.3325980.28321950X-RAY DIFFRACTION98
2.2379-2.27860.31481030.2812000X-RAY DIFFRACTION98
2.2786-2.32240.3577980.26851960X-RAY DIFFRACTION98
2.3224-2.36970.30671010.27961988X-RAY DIFFRACTION98
2.3697-2.42120.3763970.28891964X-RAY DIFFRACTION98
2.4212-2.47750.32461040.27541996X-RAY DIFFRACTION98
2.4775-2.53940.3036950.28071967X-RAY DIFFRACTION98
2.5394-2.6080.27081020.27491976X-RAY DIFFRACTION98
2.608-2.68460.33611020.25871980X-RAY DIFFRACTION98
2.6846-2.77110.29411010.2581960X-RAY DIFFRACTION98
2.7711-2.870.32721020.25471984X-RAY DIFFRACTION98
2.87-2.98470.3863980.25322006X-RAY DIFFRACTION98
2.9847-3.12030.27980.23361996X-RAY DIFFRACTION98
3.1203-3.28440.30711010.21391987X-RAY DIFFRACTION98
3.2844-3.48970.23791020.18932010X-RAY DIFFRACTION98
3.4897-3.75820.26331020.16951982X-RAY DIFFRACTION98
3.7582-4.13470.2101980.15881993X-RAY DIFFRACTION98
4.1347-4.72910.17211000.13281985X-RAY DIFFRACTION98
4.7291-5.94360.216960.17322014X-RAY DIFFRACTION98
5.9436-24.19460.2563980.18842034X-RAY DIFFRACTION98

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