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- PDB-8hko: Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain b... -

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Basic information

Entry
Database: PDB / ID: 8hko
TitleMutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Rucaparib
ComponentsPoly [ADP-ribose] polymerase 2
KeywordsTRANSFERASE / DNA ADP-ribosyltransferase 2 / PARP2 / Rucaparib
Function / homology
Function and homology information


hippocampal neuron apoptotic process / response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / HDR through MMEJ (alt-NHEJ) ...hippocampal neuron apoptotic process / response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / HDR through MMEJ (alt-NHEJ) / poly-ADP-D-ribose modification-dependent protein binding / DNA repair-dependent chromatin remodeling / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / site of DNA damage / NAD+-protein ADP-ribosyltransferase activity / decidualization / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleosome binding / POLB-Dependent Long Patch Base Excision Repair / extrinsic apoptotic signaling pathway / nucleotidyltransferase activity / DNA Damage Recognition in GG-NER / base-excision repair / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / double-strand break repair / damaged DNA binding / DNA repair / DNA damage response / chromatin binding / nucleolus / nucleoplasm / nucleus
Similarity search - Function
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. / Poly(ADP-ribose) polymerase catalytic domain ...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. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile.
Similarity search - Domain/homology
Rucaparib / Poly [ADP-ribose] polymerase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, X.Y. / Zhou, J. / Xu, B.L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82003657 China
National Natural Science Foundation of China (NSFC)81673300 China
National Natural Science Foundation of China (NSFC)82173693 China
CitationJournal: To Be Published
Title: Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Rucaparib
Authors: Wang, X.Y. / Zhou, J. / Xu, B.L.
History
DepositionNov 27, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 2
B: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,13110
Polymers79,9322
Non-polymers1,1998
Water10,665592
1
A: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7507
Polymers39,9661
Non-polymers7846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3813
Polymers39,9661
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.761, 86.286, 96.047
Angle α, β, γ (deg.)90.000, 90.390, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Poly [ADP-ribose] polymerase 2 / PARP-2 / hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / DNA ADP- ...PARP-2 / hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / DNA ADP-ribosyltransferase PARP2 / NAD(+) ADP-ribosyltransferase 2 / ADPRT-2 / Poly[ADP-ribose] synthase 2 / pADPRT-2 / Protein poly-ADP-ribosyltransferase PARP2


Mass: 39965.910 Da / Num. of mol.: 2 / Mutation: T349S,L351R,S353G,P354L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP2, ADPRT2, ADPRTL2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UGN5, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-RPB / Rucaparib / Rucaparib


Mass: 323.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18FN3O / Feature type: SUBJECT OF INVESTIGATION / Comment: anticancer, inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 25% PEG-3350, 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→36.65 Å / Num. obs: 37874 / % possible obs: 99.85 % / Redundancy: 5.9 % / Biso Wilson estimate: 21.34 Å2 / CC1/2: 0.997 / Net I/σ(I): 17.08
Reflection shellResolution: 2.1→2.175 Å / Mean I/σ(I) obs: 5.5 / Num. unique obs: 3743 / CC1/2: 0.942 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold model

Resolution: 2.1→36.65 Å / SU ML: 0.2222 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.082
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2108 1887 4.98 %
Rwork0.1635 35984 -
obs0.1659 37871 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.86 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5604 0 84 592 6280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00975806
X-RAY DIFFRACTIONf_angle_d1.41657832
X-RAY DIFFRACTIONf_chiral_restr0.078844
X-RAY DIFFRACTIONf_plane_restr0.02431008
X-RAY DIFFRACTIONf_dihedral_angle_d15.82692198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.26381560.18922711X-RAY DIFFRACTION99.97
2.16-2.220.23621590.17842770X-RAY DIFFRACTION100
2.22-2.290.24121250.17682759X-RAY DIFFRACTION100
2.29-2.370.25051480.16712772X-RAY DIFFRACTION99.9
2.37-2.470.22931200.1692784X-RAY DIFFRACTION100
2.47-2.580.22611420.16542745X-RAY DIFFRACTION99.97
2.58-2.720.20811580.16092760X-RAY DIFFRACTION100
2.72-2.890.21561550.16242766X-RAY DIFFRACTION100
2.89-3.110.2351260.16462770X-RAY DIFFRACTION99.9
3.11-3.420.19011460.15162773X-RAY DIFFRACTION99.97
3.42-3.920.18831510.14492773X-RAY DIFFRACTION99.56
3.92-4.930.171450.14552797X-RAY DIFFRACTION99.73
4.93-36.650.22581560.19462804X-RAY DIFFRACTION99.36

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