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- PDB-3v2b: Human poly(adp-ribose) polymerase 15 (ARTD7, BAL3), macro domain ... -

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Basic information

Entry
Database: PDB / ID: 3v2b
TitleHuman poly(adp-ribose) polymerase 15 (ARTD7, BAL3), macro domain 2 in complex with adenosine-5-diphosphoribose
ComponentsPoly [ADP-ribose] polymerase 15
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / POLY (ADP-RIBOSE) POLYMERASE / ADP-RIBOSE / BAL3 / B-AGGRESSIVE LYMPHOMA PROTEIN 3 / GLYCOSYLTRANSFERASE / NUCLEUS / TRANSCRIPTION / TRANSCRIPTION REGULATION / ADP-RIBOSYLATION
Function / homology
Function and homology information


protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
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. / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like ...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. / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AR6 / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKarlberg, T. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Karlberg, T. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Kotenyova, T. / Kotzcsh, A. / Kraulis, P. / Nielsen, T.K. / Nordlund, P. / Nyman, T. / Persson, C. / Roos, A.K. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van den berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Schuler, H. / Structural Genomics Consortium (SGC)
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. / Verheugd, P. / Kursula, P. / Nijmeijer, B. / Kremmer, E. / Kleine, H. / Ladurner, A.G. / Schuler, H. / Luscher, B.
History
DepositionDec 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
SupersessionFeb 6, 2013ID: 3KH6
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Revision 1.3May 29, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_prop.biol_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1502
Polymers21,5911
Non-polymers5591
Water1,72996
1
A: Poly [ADP-ribose] polymerase 15
hetero molecules

A: Poly [ADP-ribose] polymerase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3004
Polymers43,1812
Non-polymers1,1192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2090 Å2
ΔGint-12 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.102, 91.187, 62.851
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 15 / PARP-15 / B-aggressive lymphoma protein 3


Mass: 21590.600 Da / Num. of mol.: 1 / Fragment: MACRO DOMAIN 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAL3, PARP15 / Plasmid: PNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 PRARE / References: UniProt: Q460N3, 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 / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% PEG6000, 0.1M NA-ACETATE, 0.2M NaCl, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 2, 2009 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. all: 10255 / Num. obs: 10255 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.127 / Rsym value: 0.12 / Net I/σ(I): 13.9
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.417 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
BALBESphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SPV

1spv


Resolution: 2.2→34.05 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.287 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.243 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23823 513 5 %RANDOM
Rwork0.17327 ---
all0.17648 9742 --
obs0.17648 9742 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.384 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å20 Å2
2---0.66 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 36 96 1468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221420
X-RAY DIFFRACTIONr_bond_other_d0.0020.02940
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9951936
X-RAY DIFFRACTIONr_angle_other_deg0.9343.0022301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35724.90955
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1515247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.914157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211548
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02258
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_it0.881.5889
X-RAY DIFFRACTIONr_mcbond_other0.1971.5361
X-RAY DIFFRACTIONr_mcangle_it1.6321452
X-RAY DIFFRACTIONr_scbond_it2.5383531
X-RAY DIFFRACTIONr_scangle_it4.234.5481
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 37 -
Rwork0.181 700 -
obs--100 %

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