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- PDB-5ail: Human PARP9 2nd macrodomain -

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Basic information

Entry
Database: PDB / ID: 5ail
TitleHuman PARP9 2nd macrodomain
ComponentsPOLY [ADP-RIBOSE] POLYMERASE 9
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


regulation of response to type II interferon / NAD+-protein-C-terminal glycine ADP-ribosyltransferase activity / ADP-D-ribose binding / positive regulation of type II interferon-mediated signaling pathway / NAD biosynthesis via nicotinamide riboside salvage pathway / negative regulation of catalytic activity / Nicotinamide salvaging / Maturation of nucleoprotein / positive regulation of chromatin binding / enzyme inhibitor activity ...regulation of response to type II interferon / NAD+-protein-C-terminal glycine ADP-ribosyltransferase activity / ADP-D-ribose binding / positive regulation of type II interferon-mediated signaling pathway / NAD biosynthesis via nicotinamide riboside salvage pathway / negative regulation of catalytic activity / Nicotinamide salvaging / Maturation of nucleoprotein / positive regulation of chromatin binding / enzyme inhibitor activity / Maturation of nucleoprotein / post-transcriptional regulation of gene expression / STAT family protein binding / ubiquitin-like protein ligase binding / NAD+-protein ADP-ribosyltransferase activity / site of DNA damage / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of defense response to virus by host / nucleotidyltransferase activity / DNA damage checkpoint signaling / positive regulation of protein localization to nucleus / transcription corepressor activity / cell migration / double-strand break repair / histone binding / defense response to virus / viral protein processing / negative regulation of gene expression / innate immune response / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / mitochondrion / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 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 / 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
PHOSPHATE ION / Protein mono-ADP-ribosyltransferase PARP9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSieg, C. / Shrestha, L. / Talon, R. / Sorrell, F. / Williams, E. / von Delft, F. / Bountra, C. / Arrowsmith, C. / Edwards, A.M. / Knapp, S. / Elkins, J.M.
CitationJournal: To be Published
Title: Structure of Parp9 2Nd Macrodomain
Authors: Elkins, J.M.
History
DepositionFeb 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Jan 10, 2024Group: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 9
B: POLY [ADP-RIBOSE] POLYMERASE 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,49414
Polymers42,2472
Non-polymers5,24712
Water6,792377
1
A: POLY [ADP-RIBOSE] POLYMERASE 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4026
Polymers21,1241
Non-polymers3,2795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: POLY [ADP-RIBOSE] POLYMERASE 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0928
Polymers21,1241
Non-polymers1,9687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.489, 74.010, 94.369
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 273 - 455 / Label seq-ID: 1 - 183

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (1, 0.00125, 0.00119), (-0.00125, 0.99999, 0.0037), (-0.00119, -0.0037, 0.99999)
Vector: 23.46435, 0.11643, -46.97213)

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Components

#1: Protein POLY [ADP-RIBOSE] POLYMERASE 9 / PARP-9 / ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 9 / ARTD9 / B AGGRESSIVE LYMPHOMA PROTEIN / PARP9


Mass: 21123.674 Da / Num. of mol.: 2 / Fragment: 2ND MACRODOMAIN, UNP RESIDUES 310-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IXQ6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.42 Å3/Da / Density % sol: 49.2 % / Description: NONE
Crystal growpH: 6 / Details: 30% PEG1000, 0.1M SPG PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9181
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9181 Å / Relative weight: 1
ReflectionResolution: 1.55→22.73 Å / Num. obs: 58370 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.1
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.7 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q71

3q71


Resolution: 1.55→58.24 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.211 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21507 2908 5 %RANDOM
Rwork0.16921 ---
obs0.17149 55395 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.216 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---1.08 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.55→58.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2838 0 117 377 3332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193084
X-RAY DIFFRACTIONr_bond_other_d0.0040.023058
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9774158
X-RAY DIFFRACTIONr_angle_other_deg1.05337079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7335384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23925.826115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.09115549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg41.107152
X-RAY DIFFRACTIONr_chiral_restr0.0850.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023326
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02644
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_it1.7531.5981490
X-RAY DIFFRACTIONr_mcbond_other1.7461.5951489
X-RAY DIFFRACTIONr_mcangle_it2.2172.3881870
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7662.091594
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.74536139
X-RAY DIFFRACTIONr_sphericity_free34.2585107
X-RAY DIFFRACTIONr_sphericity_bonded9.43556351
Refine LS restraints NCS

Ens-ID: 1 / Number: 22872 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 211 -
Rwork0.317 4054 -
obs--97.42 %

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