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- PDB-6hxs: Human PARP16 (ARTD15) IN COMPLEX WITH CARBA-NAD -

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Basic information

Entry
Database: PDB / ID: 6hxs
TitleHuman PARP16 (ARTD15) IN COMPLEX WITH CARBA-NAD
ComponentsMono [ADP-ribose] polymerase PARP16
KeywordsTRANSFERASE / ADP-RIBOSE / PARP16 / ARTD15 / ADP-RIBOSYLATION / CARBA-NAD / SUBSTRATE
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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / 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
ADENOSINE / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Protein mono-ADP-ribosyltransferase PARP16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKarlberg, T. / Pinto, A.F. / Thorsell, A.G. / Schuler, H.
CitationJournal: To Be Published
Title: Human PARP16 (ARTD15) IN COMPLEX WITH CARBA-NAD
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 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)102,6239
Polymers100,7473
Non-polymers1,8766
Water3,873215
1
A: Mono [ADP-ribose] polymerase PARP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4334
Polymers33,5821
Non-polymers8513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mono [ADP-ribose] polymerase PARP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3413
Polymers33,5821
Non-polymers7592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mono [ADP-ribose] polymerase PARP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8492
Polymers33,5821
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.890, 147.890, 100.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 3 molecules ABC

#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

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Non-polymers , 5 types, 221 molecules

#2: Chemical ChemComp-CNA / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 662.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H30N7O13P2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 16% Poly(ethylene glycol) 3350, 0.4M sodium sulfate, 3mM Carba-NAD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.05→29.82 Å / Num. obs: 70027 / % possible obs: 100 % / Observed criterion σ(F): 9 / Redundancy: 26.4 % / Biso Wilson estimate: 40.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.166 / Rrim(I) all: 0.172 / Net I/σ(I): 15.5
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 23.1 % / Rmerge(I) obs: 2.501 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5104 / CC1/2: 0.582 / Rrim(I) all: 2.635 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia2data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F0D

4f0d


Resolution: 2.05→29.82 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.125
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3516 5.03 %RANDOM
Rwork0.197 ---
obs0.198 69930 100 %-
Displacement parametersBiso mean: 51.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.3657 Å20 Å20 Å2
2---0.3657 Å20 Å2
3---0.7314 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2.05→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5621 0 123 215 5959
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015898HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.968011HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2616SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes14HARMONIC2
X-RAY DIFFRACTIONt_gen_planes991HARMONIC5
X-RAY DIFFRACTIONt_it5898HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion2.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion747SEMIHARMONIC5
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_contact6461SEMIHARMONIC4
LS refinement shellResolution: 2.05→2.06 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2366 -5.08 %
Rwork0.2389 1328 -
all0.2388 1399 -
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)
10.6995-0.26260.13421.5873-0.51571.90330.00330.12770.0122-0.18870.03720.0692-0.0166-0.127-0.0405-0.06860.01210.0008-0.04660.0322-0.12226.9287-27.09354.1369
23.6928-0.316-0.38131.2867-0.16181.2629-0.1101-0.3679-0.30960.03050.0221-0.19440.14180.24990.088-0.16630.00760.0212-0.06040.0494-0.1064-11.0455-42.2865-1.7126
31.4154-0.49710.23242.18320.16271.91460.04920.07390.2348-0.2049-0.0704-0.2926-0.043-0.02910.0213-0.10060.01820.0127-0.1050.1182-0.090830.99223.1551-6.4492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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