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- PDB-4abk: HUMAN PARP14 (ARTD8, BAL2) - MACRO DOMAIN 3 IN COMPLEX WITH ADENO... -

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Basic information

Entry
Database: PDB / ID: 4abk
TitleHUMAN PARP14 (ARTD8, BAL2) - MACRO DOMAIN 3 IN COMPLEX WITH ADENOSINE- 5-DIPHOSPHORIBOSE
ComponentsPOLY [ADP-RIBOSE] POLYMERASE 14
KeywordsTRANSFERASE / PARP14 / ARTD8
Function / homology
Function and homology information


negative regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-4-mediated signaling pathway / : / Maturation of nucleoprotein / Maturation of nucleoprotein / positive regulation of tyrosine phosphorylation of STAT protein / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein mono-ADP-ribosyltransferase activity ...negative regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-4-mediated signaling pathway / : / Maturation of nucleoprotein / Maturation of nucleoprotein / positive regulation of tyrosine phosphorylation of STAT protein / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
PARP-14, RNA recognition motif 2 / : / : / : / : / : / : / : / : / Parp14 WWE domain ...PARP-14, RNA recognition motif 2 / : / : / : / : / : / : / : / : / Parp14 WWE domain / PARP14, first type I KH domain / PARP14, second RRM domain / PARP14, second type I KH domain / PARP14, third type I KH domain / PARP14, fourth type I KH domain / PARP14, fifth type I KH domain / PARP14, sixth type I KH domain / : / PAR14-like, first RRM domain / PARP14, third RRM domain / : / PARP14-like, eighth type I KH domain / : / WWE domain superfamily / WWE domain / WWE domain profile. / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Nucleotide-binding alpha-beta plait domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AR6 / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKarlberg, T. / Moche, M. / Thorsell, A.G. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Weigelt, J. / Schuler, H.
CitationJournal: Structure / Year: 2013
Title: Recognition of Mono-Adp-Ribosylated Artd10 Substrates by Artd8 Macrodomains
Authors: Forst, A.H. / Karlberg, T. / Herzog, N. / Thorsell, A.G. / Gross, A. / Feijs, K.L.H. / Verheugd, P. / Kursula, P. / Nijmeijer, B. / Kremmer, E. / Kleine, H. / Ladurner, A.G. / Schuler, H. / Luscher, B.
History
DepositionDec 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Mar 20, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3682
Polymers19,8091
Non-polymers5591
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.949, 41.253, 108.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein POLY [ADP-RIBOSE] POLYMERASE 14 / ADP-RIBOSE TRANSFERASE / PARP-14 / B AGGRESSIVE LYMPHOMA PROTEIN 2


Mass: 19808.555 Da / Num. of mol.: 1 / Fragment: MACRO DOMAIN 3, RESIDUES 1208-1388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.86 Å3/Da / Density % sol: 33.94 % / Description: NONE
Crystal growDetails: 1.4M TRI-SODIUM CITRATE, 0.1M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2010 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.6→35 Å / Num. obs: 18999 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 43.8
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 9.6 / % possible all: 64.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KH6

3kh6
PDB Unreleased entry


Resolution: 1.6→32.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.366 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 950 5 %RANDOM
Rwork0.16635 ---
obs0.16835 18049 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.599 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å20 Å2
2---1.41 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 36 135 1543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221465
X-RAY DIFFRACTIONr_bond_other_d0.0020.02975
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9881990
X-RAY DIFFRACTIONr_angle_other_deg0.8753.0022398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5175195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36326.45262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68515265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.433154
X-RAY DIFFRACTIONr_chiral_restr0.0890.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021628
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02259
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.91.5919
X-RAY DIFFRACTIONr_mcbond_other0.251.5381
X-RAY DIFFRACTIONr_mcangle_it1.67421488
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5723546
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3694.5495
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 47 -
Rwork0.179 896 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 7.8748 Å / Origin y: 10.1981 Å / Origin z: -13.6939 Å
111213212223313233
T0.0135 Å2-0.0004 Å2-0.0052 Å2-0.0232 Å20.0088 Å2--0.006 Å2
L0.1459 °2-0.0455 °2-0.1016 °2-0.7809 °2-0.0649 °2--0.5942 °2
S0.0267 Å °0.0121 Å °0.0009 Å °0.0175 Å °-0.0159 Å °-0.0293 Å °-0.0245 Å °-0.0245 Å °-0.0108 Å °

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