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- PDB-6fxi: Human PARP10 (ARTD10), catalytic fragment in complex with 3-amino... -

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Basic information

Entry
Database: PDB / ID: 6fxi
TitleHuman PARP10 (ARTD10), catalytic fragment in complex with 3-aminobenzamide and citrate
ComponentsPoly [ADP-ribose] polymerase 10
KeywordsTRANSFERASE / Transferase domain / ADP-ribosylation / PARP inhibitor
Function / homology
Function and homology information


negative regulation of protein K63-linked ubiquitination / NAD+- protein-lysine ADP-ribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / K63-linked polyubiquitin modification-dependent protein binding / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / negative regulation of NF-kappaB transcription factor activity ...negative regulation of protein K63-linked ubiquitination / NAD+- protein-lysine ADP-ribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / K63-linked polyubiquitin modification-dependent protein binding / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / negative regulation of NF-kappaB transcription factor activity / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / translesion synthesis / negative regulation of fibroblast proliferation / nucleotidyltransferase activity / transcription corepressor activity / chromatin organization / DNA-binding transcription factor binding / viral protein processing / negative regulation of gene expression / nucleolus / Golgi apparatus / nucleus / cytosol / cytoplasm
Similarity search - Function
PARP-10, RNA recognition motif 1 and 2 / 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. / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3-aminobenzamide / CITRIC ACID / Protein mono-ADP-ribosyltransferase PARP10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKarlberg, T. / Thorsell, A.G. / Schuler, H.
CitationJournal: To Be Published
Title: Human PARP10 (ARTD10), catalytic fragment in complex with 3-aminobenzamide and citrate
Authors: Karlberg, T. / Thorsell, A.G. / Schuler, H.
History
DepositionMar 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 10
B: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0067
Polymers43,2572
Non-polymers7495
Water81145
1
A: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0494
Polymers21,6291
Non-polymers4203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9573
Polymers21,6291
Non-polymers3282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.600, 86.600, 57.460
Angle α, β, γ (deg.)90.00, 104.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly [ADP-ribose] polymerase 10 / PARP-10 / ADP-ribosyltransferase diphtheria toxin-like 10 / ARTD10


Mass: 21628.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP10 / Plasmid: pNIC-Bsa28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53GL7, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-3AB / 3-aminobenzamide / 3-Aminobenzamide


Mass: 136.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2O
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 16% PEG3350, 0.1 M Citrate-Bis-Tris-Propane, 3 mM 3-aminobenzamide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→49.85 Å / Num. obs: 15114 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 50.17 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.223 / Rrim(I) all: 0.242 / Net I/σ(I): 7.9
Reflection shellResolution: 2.6→2.71 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.737 / Num. unique obs: 1747 / CC1/2: 0.864 / Rrim(I) all: 0.797 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LX6

5lx6


Resolution: 2.6→49.85 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.853 / SU R Cruickshank DPI: 0.593 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.541 / SU Rfree Blow DPI: 0.28 / SU Rfree Cruickshank DPI: 0.289
RfactorNum. reflection% reflectionSelection details
Rfree0.245 756 5 %RANDOM
Rwork0.21 ---
obs0.212 15113 99.7 %-
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.4714 Å20 Å2-10.3916 Å2
2--9.1798 Å20 Å2
3----15.6512 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.6→49.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 52 45 3119
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013141HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.124261HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1435SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes6HARMONIC2
X-RAY DIFFRACTIONt_gen_planes549HARMONIC5
X-RAY DIFFRACTIONt_it3141HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion3.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion383SEMIHARMONIC5
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_contact3400SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2826 135 5.01 %
Rwork0.2488 2559 -
all0.2505 2694 -
obs--98.47 %
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)
12.21192.33930.24463.8474-0.04731.0524-0.11350.0179-0.369-0.16010.0256-0.58620.06910.08230.0878-0.12510.01720.0424-0.14370.00210.051-9.041521.311569.4993
22.43982.03150.0673.58830.52991.0308-0.23150.10060.2242-0.37150.18340.0694-0.1905-0.02460.0481-0.0683-0.0091-0.0334-0.1269-0.0061-0.0346-10.850451.651971.7283
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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