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- PDB-4abl: HUMAN PARP14 (ARTD8, BAL2) - MACRO DOMAIN 3 -

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Basic information

Entry
Database: PDB / ID: 4abl
TitleHUMAN PARP14 (ARTD8, BAL2) - MACRO DOMAIN 3
ComponentsPOLY [ADP-RIBOSE] POLYMERASE 14
KeywordsTRANSFERASE / PARP14
Function / homology
Function and homology information


negative regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-4-mediated signaling pathway / Nicotinamide salvage / Maturation of nucleoprotein / Maturation of nucleoprotein / positive regulation of tyrosine phosphorylation of STAT protein / protein poly-ADP-ribosylation / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE2 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE18 glutamate ADP-ribosyltransferase activity ...negative regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-4-mediated signaling pathway / Nicotinamide salvage / Maturation of nucleoprotein / Maturation of nucleoprotein / positive regulation of tyrosine phosphorylation of STAT protein / protein poly-ADP-ribosylation / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE2 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE18 glutamate ADP-ribosyltransferase activity / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PARP-14, RNA recognition motif 2 / : / Parp14 WWE 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 ...PARP-14, RNA recognition motif 2 / : / Parp14 WWE 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 / Macro domain profile. / Macro domain-like / Nucleotide-binding alpha-beta plait domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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)19,8882
Polymers19,8091
Non-polymers801
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.705, 41.066, 108.918
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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 1.9 Å3/Da / Density % sol: 35.35 % / Description: NONE
Crystal growDetails: 30% PEGMME2000, 0.05M POTASSIUM BROMIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 26, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.15→35 Å / Num. obs: 53461 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.9
Reflection shellResolution: 1.15→1.18 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.9 / % possible all: 82.7

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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 4ABK

4abk


Resolution: 1.15→32.79 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.258 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19132 2673 5 %RANDOM
Rwork0.16067 ---
obs0.16222 50788 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: 15.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2---0.81 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.15→32.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 1 199 1571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221439
X-RAY DIFFRACTIONr_bond_other_d0.0010.02988
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9591949
X-RAY DIFFRACTIONr_angle_other_deg0.90532457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8365200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.90726.27159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46615278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.282154
X-RAY DIFFRACTIONr_chiral_restr0.10.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021619
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02261
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_it1.6781.5923
X-RAY DIFFRACTIONr_mcbond_other0.5591.5382
X-RAY DIFFRACTIONr_mcangle_it2.54121501
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.733516
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.414.5438
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.43532427
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 165 -
Rwork0.208 3136 -
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)
10.4426-0.7083-0.21631.13440.34570.10590.01980.0227-0.0359-0.0283-0.03990.0552-0.0113-0.00960.02010.03490.0004-0.00310.0366-0.00160.034120.857245.853718.2394
20.04180.0351-0.01970.2608-0.09890.18180.00490.00540.00360.00430.0031-0.00210.0181-0.0212-0.0080.0322-0.0025-0.00050.0380.00180.03121.149626.432614.2006
33.9328-0.4798-0.10771.6984-1.39231.21730.0620.083-0.1667-0.629-0.02380.01840.5358-0.0312-0.03820.2441-0.0191-0.01220.02410.00780.03125.809913.84745.4382
40.0163-0.01860.01240.176-0.00810.06020.00180.00910.00720.0188-0.0026-0.00740.00710.00030.00080.0327-0.001-0.00010.03620.00140.03227.567932.710614.5287
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1208 - 1223
2X-RAY DIFFRACTION2A1224 - 1263
3X-RAY DIFFRACTION3A1264 - 1283
4X-RAY DIFFRACTION4A1284 - 1388

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