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- PDB-7f42: PARP15 catalytic domain in complex with Iniparib -

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Basic information

Entry
Database: PDB / ID: 7f42
TitlePARP15 catalytic domain in complex with Iniparib
ComponentsProtein mono-ADP-ribosyltransferase PARP15
KeywordsTRANSFERASE / Glycosyltransferase / mono-ADP-ribosyltransferase 15
Function / homology
Function and homology information


protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ 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
Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like
Similarity search - Domain/homology
4-iodo-3-nitrobenzamide / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsZhou, X.L. / Zhou, H. / Li, J. / Zhang, J.
CitationJournal: To Be Published
Title: PARP15 catalytic domain in complex with Iniparib
Authors: Zhou, X.L. / Zhou, H. / Li, J. / Zhang, J.
History
DepositionJun 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 2.0Oct 12, 2022Group: Atomic model / Data collection / Structure summary / Category: atom_site / chem_comp / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.pdbx_synonyms / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protein mono-ADP-ribosyltransferase PARP15
A: Protein mono-ADP-ribosyltransferase PARP15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2003
Polymers45,9082
Non-polymers2921
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-10 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.307, 68.757, 158.382
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Protein mono-ADP-ribosyltransferase PARP15 / ADP-ribosyltransferase diphtheria toxin-like 7 / ARTD7 / B-aggressive lymphoma protein 3 / Poly ...ADP-ribosyltransferase diphtheria toxin-like 7 / ARTD7 / B-aggressive lymphoma protein 3 / Poly [ADP-ribose] polymerase 15 / PARP-15


Mass: 22953.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP15, BAL3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q460N3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-33E / 4-iodo-3-nitrobenzamide / Iniparib


Mass: 292.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5IN2O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM HEPES buffer,pH6.5, 22%PEG 3350, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.41→41.88 Å / Num. obs: 1244320 / % possible obs: 99.4 % / Redundancy: 13.1 % / Biso Wilson estimate: 17.6194162395 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 34.6
Reflection shellResolution: 1.41→1.49 Å / Rmerge(I) obs: 1.06 / Num. unique obs: 94885

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BLJ

3blj


Resolution: 1.41→41.88 Å / SU ML: 0.160823037035 / Cross valid method: NONE / σ(F): 1.35153805638 / Phase error: 23.6610651667
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.230489093745 4756 5.01745983184 %
Rwork0.204016284057 90033 -
obs0.205339869384 94789 98.957071867 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.1969977017 Å2
Refinement stepCycle: LAST / Resolution: 1.41→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 13 280 3467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005789973643173273
X-RAY DIFFRACTIONf_angle_d0.8888120012114443
X-RAY DIFFRACTIONf_chiral_restr0.078996265234470
X-RAY DIFFRACTIONf_plane_restr0.0051203234475582
X-RAY DIFFRACTIONf_dihedral_angle_d6.551433707851186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.42860.3099601718751360.2799642403782971X-RAY DIFFRACTION98.7603305785
1.4286-1.44540.3645453444021490.279125918922949X-RAY DIFFRACTION97.8212819703
1.4454-1.4630.309772646961440.2729368250392907X-RAY DIFFRACTION96.7649857279
1.463-1.48150.3015583669761490.2729478869862957X-RAY DIFFRACTION99.5193848126
1.4815-1.5010.2862801909421670.2665955165212939X-RAY DIFFRACTION97.3973032299
1.501-1.52160.2939077913021600.2561047956292930X-RAY DIFFRACTION98.1887511916
1.5216-1.54330.2665523861021580.2517357988012930X-RAY DIFFRACTION98.9426465876
1.5433-1.56640.2564142945741620.2316262125422935X-RAY DIFFRACTION97.0542149796
1.5664-1.59080.2871804899651670.231177090132955X-RAY DIFFRACTION99.7444089457
1.5908-1.61690.2489611385041730.229872186672930X-RAY DIFFRACTION97.2727272727
1.6169-1.64480.2524975238431620.2274568808442986X-RAY DIFFRACTION99.7781299525
1.6448-1.67470.2695692460391790.2251965808082935X-RAY DIFFRACTION97.9861548143
1.6747-1.70690.243444515341740.2239614754332932X-RAY DIFFRACTION99.5193848126
1.7069-1.74180.2631839191961540.2199376048072990X-RAY DIFFRACTION98.096723869
1.7418-1.77960.2319478683061420.2182118200952980X-RAY DIFFRACTION99.8401023345
1.7796-1.8210.2681998624081630.2164652480652992X-RAY DIFFRACTION98.3478802993
1.821-1.86660.2700338838851520.2225523684873014X-RAY DIFFRACTION99.9684243764
1.8666-1.9170.257721954671610.2205492624092978X-RAY DIFFRACTION98.7106918239
1.917-1.97340.2632336644111360.2092023560983026X-RAY DIFFRACTION98.9981214778
1.9734-2.03710.2443385246581740.2082039627742994X-RAY DIFFRACTION99.9684443042
2.0371-2.10990.1986802192931430.2071797360263022X-RAY DIFFRACTION99.2474129821
2.1099-2.19440.2381534432751520.2093987530393017X-RAY DIFFRACTION99.3105609527
2.1944-2.29430.2270732445011460.2054241363323059X-RAY DIFFRACTION99.5032598572
2.2943-2.41520.2575825627061670.2109724616923016X-RAY DIFFRACTION99.7180451128
2.4152-2.56650.2264643273611590.2111915763863041X-RAY DIFFRACTION99.8128509046
2.5665-2.76470.2140426945711610.2056470500163068X-RAY DIFFRACTION99.8762759047
2.7647-3.04280.2249183122861720.2090239909793083X-RAY DIFFRACTION99.8466257669
3.0428-3.48290.247539752761770.1951029359523085X-RAY DIFFRACTION99.9081163859
3.4829-4.38740.1905605487961600.1681061265483133X-RAY DIFFRACTION99.8483929654
4.3874-41.880.1785329503661570.1762508926673279X-RAY DIFFRACTION99.0201729107

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