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- PDB-4f0d: Human ARTD15/PARP16 IN COMPLEX WITH 3-AMINOBENZAMIDE -

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Basic information

Entry
Database: PDB / ID: 4f0d
TitleHuman ARTD15/PARP16 IN COMPLEX WITH 3-AMINOBENZAMIDE
ComponentsPoly [ADP-ribose] polymerase 16
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / ADP-RIBOSE / PARP16 / ARTD15 / Structural Genomics / Structural Genomics Consortium / SGC / ARTD Transferase domain / ADP-ribosylation / TRANSFERASE-TRANSFERASE 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
3-aminobenzamide / Protein mono-ADP-ribosyltransferase PARP16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.7 Å
AuthorsKarlberg, T. / Thorsell, A.G. / Kallas, A. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of Human ADP-ribose Transferase ARTD15/PARP16 Reveals a Novel Putative Regulatory Domain.
Authors: Karlberg, T. / Thorsell, A.G. / Kallas, A. / Schuler, H.
History
DepositionMay 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 16
B: Poly [ADP-ribose] polymerase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3573
Polymers62,2212
Non-polymers1361
Water00
1
A: Poly [ADP-ribose] polymerase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2472
Polymers31,1111
Non-polymers1361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly [ADP-ribose] polymerase 16


Theoretical massNumber of molelcules
Total (without water)31,1111
Polymers31,1111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.824, 195.349, 60.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Poly [ADP-ribose] polymerase 16 / PARP-16


Mass: 31110.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C15orf30, PARP16 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q8N5Y8, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-3AB / 3-aminobenzamide


Mass: 136.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2O

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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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.6
Details: 22% PEG 3350, 200 mM di-ammonium tartrate, 0.2 M NaCl, 20% glycerol, pH 6.6, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.94861 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 10, 2011 / Details: mirrors
RadiationMonochromator: Si-111 crystal (double crystal monochromator)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94861 Å / Relative weight: 1
ReflectionResolution: 2.6→35 Å / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 67.47 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 25.3
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoSHARPphasing
BUSTER2.11.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.7→33.63 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.8462 / SU R Cruickshank DPI: 0.366 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2871 982 5 %RANDOM
Rwork0.2463 ---
obs0.2483 19621 99.98 %-
all-21914 --
Displacement parametersBiso mean: 63.47 Å2
Baniso -1Baniso -2Baniso -3
1--2.6696 Å20 Å20 Å2
2--8.0289 Å20 Å2
3----5.3594 Å2
Refine analyzeLuzzati coordinate error obs: 0.464 Å
Refinement stepCycle: LAST / Resolution: 2.7→33.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3057 0 10 0 3067
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013142HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.124267HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1378SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes469HARMONIC5
X-RAY DIFFRACTIONt_it3142HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion3.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion409SEMIHARMONIC5
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_contact3373SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.85 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.312 142 5.03 %
Rwork0.2465 2682 -
all0.2495 2824 -
obs--99.98 %
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)
12.51620.25370.76291.83120.28984.11820.0505-0.0520.1135-0.0545-0.0886-0.071-0.1057-0.13690.0382-0.2846-0.02220.0439-0.0823-0.0352-0.117515.124445.401211.4245
22.32610.50680.7814.41391.9532.3456-0.14150.2319-0.4093-0.56770.1448-0.2290.45780.3213-0.00330.12690.05620.1767-0.3314-0.1035-0.041820.224612.4462-9.0773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|4 - A|273 }A4 - 273
2X-RAY DIFFRACTION2{ B|4 - B|273 }B4 - 273

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