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- PDB-6hxr: Human PARP16 (ARTD15) IN COMPLEX WITH EB-47 -

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Basic information

Entry
Database: PDB / ID: 6hxr
TitleHuman PARP16 (ARTD15) IN COMPLEX WITH EB-47
ComponentsMono [ADP-ribose] polymerase PARP16
KeywordsTRANSFERASE / ADP-RIBOSE / PARP16 / ARTD15 / ADP-RIBOSYLATION / EB-47 / INHIBITOR COMPLEX
Function / homology
Function and homology information


endoplasmic reticulum tubular network / NAD+-protein-lysine ADP-ribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein auto-ADP-ribosylation / IRE1-mediated unfolded protein response ...endoplasmic reticulum tubular network / NAD+-protein-lysine ADP-ribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein auto-ADP-ribosylation / IRE1-mediated unfolded protein response / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / negative regulation of cytoplasmic translation / endoplasmic reticulum unfolded protein response / nucleotidyltransferase activity / protein serine/threonine kinase activator activity / cellular response to leukemia inhibitory factor / kinase binding / nuclear envelope / viral protein processing / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / cytosol
Similarity search - Function
PARP16 N-terminal domain / : / ARTD15 N-terminal domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile.
Similarity search - Domain/homology
Chem-UHB / Protein mono-ADP-ribosyltransferase PARP16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKarlberg, T. / Pinto, A.F. / Thorsell, A.G. / Schuler, H.
CitationJournal: To Be Published
Title: Human PARP16 (ARTD15) IN COMPLEX WITH EB-47
Authors: Karlberg, T. / Pinto, A.F. / Thorsell, A.G. / Schuler, H.
History
DepositionOct 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: 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
A: Mono [ADP-ribose] polymerase PARP16
B: Mono [ADP-ribose] polymerase PARP16
C: Mono [ADP-ribose] polymerase PARP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8225
Polymers100,7473
Non-polymers1,0752
Water00
1
A: Mono [ADP-ribose] polymerase PARP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1202
Polymers33,5821
Non-polymers5381
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mono [ADP-ribose] polymerase PARP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1202
Polymers33,5821
Non-polymers5381
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mono [ADP-ribose] polymerase PARP16


Theoretical massNumber of molelcules
Total (without water)33,5821
Polymers33,5821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.064, 148.064, 99.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Mono [ADP-ribose] polymerase PARP16 / ADP-ribosyltransferase diphtheria toxin-like 15 / Poly [ADP-ribose] polymerase 16 / PARP-16


Mass: 33582.242 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP16, ARTD15, C15orf30 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N5Y8, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-UHB / 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide


Mass: 537.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27N9O6

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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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% Poly(ethylene glycol) 3350, 0.2M ammonium acetate, 0.1M Bis-Tris, 1mM EB-47

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.9→49.4 Å / Num. obs: 25189 / % possible obs: 99.9 % / Redundancy: 29.5 % / Biso Wilson estimate: 92.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.223 / Net I/σ(I): 20.9
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 29.7 % / Rmerge(I) obs: 2.25 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3968 / CC1/2: 0.716 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F0D

4f0d


Resolution: 2.9→33.7 Å / Cor.coef. Fo:Fc: 0.9329 / Cor.coef. Fo:Fc free: 0.9137 / SU R Cruickshank DPI: 0.844 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.805 / SU Rfree Blow DPI: 0.308 / SU Rfree Cruickshank DPI: 0.315
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 1256 5 %RANDOM
Rwork0.1993 ---
obs0.2009 25112 99.99 %-
Displacement parametersBiso mean: 91.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.9449 Å20 Å20 Å2
2--0.9449 Å20 Å2
3----1.8898 Å2
Refine analyzeLuzzati coordinate error obs: 0.373 Å
Refinement stepCycle: 1 / Resolution: 2.9→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5543 0 78 0 5621
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125777HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.267843HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2562SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes133HARMONIC2
X-RAY DIFFRACTIONt_gen_planes859HARMONIC5
X-RAY DIFFRACTIONt_it5777HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.46
X-RAY DIFFRACTIONt_other_torsion3.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion726SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6195SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.02 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3127 140 5.02 %
Rwork0.2599 2649 -
all0.2625 2789 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.47590.76521.11583.4277-0.23863.2928-0.27290.70480.2408-0.54060.11280.2007-0.18480.13930.1601-0.1864-0.0494-0.0089-0.0630.148-0.2308175.023121.54104.452
27.3316-0.42250.51222.0789-0.24692.2394-0.1576-0.3829-0.64650.06880.074-0.2320.22870.29410.0836-0.22690.02750.0547-0.18010.0551-0.1179137.673106.17598.1945
32.3131-0.640.75683.9158-1.66364.2738-0.05430.32160.8142-0.1558-0.1815-0.4738-0.40540.08650.2357-0.3022-0.0672-0.1182-0.08110.304-0.1119179.331151.07893.0989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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