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- PDB-5qi3: PanDDA analysis group deposition of models with modelled events (... -

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Basic information

Entry
Database: PDB / ID: 5qi3
TitlePanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human PARP14 Macrodomain 3 in complex with FMOPL000475a
ComponentsPoly [ADP-ribose] polymerase 14
KeywordsTRANSFERASE / PanDDA / SGC - Diamond I04-1 fragment screening / macrodomain / XChemExplorer
Function / homology
Function and homology information


positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases ...positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / membrane / nucleus / 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 / 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. / Macro domain / Appr-1"-p processing enzyme / 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
Chem-GUY / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.05 Å
AuthorsSchuller, M. / Talon, R. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Zhang, R. / von Delft, F. / Schuler, H. / Kessler, B. / Knapp, S. ...Schuller, M. / Talon, R. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Zhang, R. / von Delft, F. / Schuler, H. / Kessler, B. / Knapp, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Elkins, J.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)
Authors: Schuller, M. / Talon, R. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Zhang, R. / von Delft, F. / Schuler, H. / Kessler, B. / Knapp, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Elkins, J.
History
DepositionMay 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)20,1795
Polymers19,8091
Non-polymers3704
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.493, 41.533, 110.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Poly [ADP-ribose] polymerase 14 / PARP-14 / ADP-ribosyltransferase diphtheria toxin-like 8 / ARTD8 / B aggressive lymphoma protein 2


Mass: 19808.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP14, BAL2, KIAA1268 / Production host: Escherichia coli (E. coli) / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GUY / ~{N}-(1-propyl-1,2,3,4-tetrazol-5-yl)furan-2-carboxamide


Mass: 221.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N5O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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 Å3/Da / Density % sol: 38.64 % / Mosaicity: 0.05 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 80 mM KBr, 30 % PEG2kMME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.05→29.29 Å / Num. obs: 60056 / % possible obs: 80.2 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071 / Net I/σ(I): 22.9 / Num. measured all: 291361 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.05-1.081.10.1378857950.9310.1370.1945.514.8
4.7-29.295.50.07953089650.9860.0370.08729.698.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ABL

4abl


Resolution: 1.05→55.5 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.715 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1576 3047 5.1 %RANDOM
Rwork0.1399 ---
obs0.1408 56943 79.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.3 Å2 / Biso mean: 12.445 Å2 / Biso min: 5.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å2-0 Å2
2---0.47 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.05→55.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 22 220 1622
Biso mean--17.36 24.05 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191553
X-RAY DIFFRACTIONr_bond_other_d0.0020.021433
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9552110
X-RAY DIFFRACTIONr_angle_other_deg0.9422.993365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7255212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01225.69265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.70215284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.533154
X-RAY DIFFRACTIONr_chiral_restr0.0920.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021827
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02296
X-RAY DIFFRACTIONr_mcbond_it0.9041.027806
X-RAY DIFFRACTIONr_mcbond_other0.9011.026805
X-RAY DIFFRACTIONr_mcangle_it1.2371.5541032
X-RAY DIFFRACTIONr_rigid_bond_restr1.02332986
X-RAY DIFFRACTIONr_sphericity_free19.3955156
X-RAY DIFFRACTIONr_sphericity_bonded6.75353018
LS refinement shellResolution: 1.051→1.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 33 -
Rwork0.251 761 -
all-794 -
obs--14.43 %

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