PDB-8adj: Poly(ADP-ribose) glycohydrolase (PARG) from Drosophila melanogast...

ID or keywords:

Entry

Database: PDB / ID: 8adj

Title

Poly(ADP-ribose) glycohydrolase (PARG) from Drosophila melanogaster in complex with PARG inhibitor PDD00017272

Components

Poly(ADP-ribose) glycohydrolase

Keywords

HYDROLASE / PARG / POLY(ADP-RIBOSE) GLYCOHYDROLASE / INHIBITOR / PDD00017272

Function / homology

Function and homology information

POLB-Dependent Long Patch Base Excision Repair / female germ-line stem cell population maintenance / Cajal body organization / nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / ATP generation from poly-ADP-D-ribose / maintenance of protein location in nucleus / regulation of RNA splicing / regulation of DNA repair ...
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.508 Å

Authors

Ariza, A. / Fontana, P.

Funding support

United Kingdom, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: Serine ADP-ribosylation in Drosophila provides insights into the evolution of reversible ADP-ribosylation signalling.
Authors: Fontana, P. / Buch-Larsen, S.C. / Suyari, O. / Smith, R. / Suskiewicz, M.J. / Schutzenhofer, K. / Ariza, A. / Rack, J.G.M. / Nielsen, M.L. / Ahel, I.

History

Deposition	Jul 8, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 14, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8adj.cif.gz	832.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8adj.ent.gz	532.1 KB	Display	PDB format
PDBx/mmJSON format	8adj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8adj_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8adj_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8adj_validation.xml.gz	57.4 KB	Display
Data in CIF	8adj_validation.cif.gz	78.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ad/8adj ftp://data.pdbj.org/pub/pdb/validation_reports/ad/8adj	HTTPS FTP

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Related structure data

Related structure data	8adkC 6hmkS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Poly(ADP-ribose) glycohydrolase

B: Poly(ADP-ribose) glycohydrolase

C: Poly(ADP-ribose) glycohydrolase

hetero molecules

201 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Poly(ADP-ribose) glycohydrolase

hetero molecules

defined by author
Evidence: gel filtration
67 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Poly(ADP-ribose) glycohydrolase

hetero molecules

defined by author
66.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Poly(ADP-ribose) glycohydrolase

hetero molecules

defined by author
66.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	93.392, 115.919, 123.267
Angle α, β, γ (deg.)	90.000, 112.205, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A

NCS domain segments:

Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 26 - 547 / Label seq-ID: 46 - 567

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	1	A	A
2	1	1	A	A
3	2	2	B - A	B - A
4	2	2	B - A	B - A
5	3	3	C - A	C - A
6	3	3	C - A	C - A

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

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Protein , 1 types, 3 molecules ABC

#1: Protein	Poly(ADP-ribose) glycohydrolase Mass: 65993.641 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Parg, CG2864 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta References: UniProt: O46043, poly(ADP-ribose) glycohydrolase

#1: Protein

Poly(ADP-ribose) glycohydrolase

Mass: 65993.641 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Drosophila melanogaster (fruit fly) / Gene: Parg, CG2864 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: O46043, poly(ADP-ribose) glycohydrolase

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Non-polymers , 5 types, 217 molecules

#2: Chemical	ChemComp-LQX / 1-[(2,5-dimethylpyrazol-3-yl)methyl]-N-(1-methylcyclopropyl)-3-[(2-methyl-1,3-thiazol-5-yl)methyl]-2,4-bis(oxidanylidene)quinazoline-6-sulfonamide Mass: 514.620 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₃H₂₆N₆O₄S₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.48 Å³/Da / Density % sol: 64.69 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 19% (v/v) PEG3350, 210 mM Na2SO4, 100 mM BisTris propane pH 7.2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97958 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97958 Å / Relative weight: 1
Reflection	Resolution: 2.508→59.02 Å / Num. obs: 83253 / % possible obs: 100 % / Redundancy: 6.7 % / CC_1/2: 0.996 / R_merge(I) obs: 0.122 / R_pim(I) all: 0.051 / R_rim(I) all: 0.132 / Net I/σ(I): 9.6
Reflection shell	Resolution: 2.51→2.58 Å / Redundancy: 6.7 % / R_merge(I) obs: 1.829 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6176 / CC_1/2: 0.511 / R_pim(I) all: 0.76 / R_rim(I) all: 1.983 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6hmk

6hmk

Resolution: 2.508→59.015 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.947 / WR_factor R_free: 0.21 / WR_factor R_work: 0.172 / SU B: 20.768 / SU ML: 0.205 / Average fsc free: 0.9557 / Average fsc work: 0.9684 / Cross valid method: FREE R-VALUE / ESU R: 0.32 / ESU R Free: 0.23
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2231	4262	5.121 %
R_work	0.1826	78963	-
all	0.185	-	-
obs	-	83225	99.789 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 68.965 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.199 Å²	0 Å²	1.02 Å²
2-	-	0.692 Å²	0 Å²
3-	-	-	-1.293 Å²

Refinement step

Cycle: LAST / Resolution: 2.508→59.015 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12501	0	168	200	12869

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	13022
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	11622
X-RAY DIFFRACTION	r_angle_refined_deg	1.681	1.646	17687
X-RAY DIFFRACTION	r_angle_other_deg	0.563	1.55	27128
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.891	5	1547
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	20.803	10	114
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.163	10	2163
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.819	10	640
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	1872
X-RAY DIFFRACTION	r_chiral_restr_other	0.127	0.2	3
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	14850
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2687
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	2413
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.197	0.2	10560
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	6058
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	6782
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	245
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.088	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.218	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.153	0.2	33
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.354	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	6.137	5.596	6182
X-RAY DIFFRACTION	r_mcbond_other	6.131	5.596	6182
X-RAY DIFFRACTION	r_mcangle_it	8.594	8.379	7719
X-RAY DIFFRACTION	r_mcangle_other	8.593	8.38	7720
X-RAY DIFFRACTION	r_scbond_it	7.149	6.036	6840
X-RAY DIFFRACTION	r_scbond_other	6.705	6.021	6817
X-RAY DIFFRACTION	r_scangle_it	9.393	8.845	9955
X-RAY DIFFRACTION	r_scangle_other	9.292	8.829	9920
X-RAY DIFFRACTION	r_lrange_it	11.051	65.215	14015
X-RAY DIFFRACTION	r_lrange_other	11.04	65.185	13993
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.064	0.05	17319
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.061	0.05	17327
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.064	0.05	17293

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.06371	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06371	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06112	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06112	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06445	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06445	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.508-2.573	0.365	314	0.33	5681	0.332	6160	0.899	0.921	97.3214	0.33
2.573-2.643	0.344	344	0.308	5617	0.31	5961	0.928	0.939	100	0.305
2.643-2.72	0.33	309	0.301	5506	0.302	5815	0.934	0.943	100	0.297
2.72-2.803	0.287	252	0.26	5388	0.261	5640	0.949	0.959	100	0.253
2.803-2.895	0.273	278	0.231	5187	0.233	5465	0.955	0.967	100	0.218
2.895-2.996	0.285	254	0.213	5055	0.216	5309	0.95	0.972	100	0.199
2.996-3.109	0.261	281	0.209	4858	0.211	5141	0.957	0.973	99.9611	0.195
3.109-3.236	0.26	265	0.202	4674	0.205	4939	0.955	0.975	100	0.188
3.236-3.379	0.254	232	0.199	4478	0.201	4710	0.965	0.978	100	0.187
3.379-3.543	0.239	230	0.202	4293	0.204	4523	0.965	0.977	100	0.191
3.543-3.734	0.223	245	0.19	4058	0.192	4303	0.972	0.982	100	0.182
3.734-3.96	0.234	212	0.182	3846	0.185	4058	0.963	0.982	100	0.175
3.96-4.232	0.194	160	0.158	3690	0.16	3850	0.978	0.986	100	0.153
4.232-4.569	0.169	198	0.129	3370	0.131	3568	0.983	0.99	100	0.127
4.569-5.002	0.17	134	0.129	3153	0.13	3287	0.984	0.99	100	0.127
5.002-5.587	0.199	143	0.149	2846	0.152	2989	0.982	0.988	100	0.146
5.587-6.442	0.195	174	0.154	2466	0.156	2640	0.982	0.987	100	0.152
6.442-7.866	0.178	110	0.156	2146	0.158	2256	0.982	0.986	100	0.158
7.866-11.027	0.126	76	0.121	1669	0.121	1745	0.99	0.991	100	0.127
11.027-59.015	0.225	51	0.223	981	0.223	1035	0.972	0.963	99.7101	0.256

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.4673	-0.1851	-0.1891	0.5347	-0.3251	0.4505	-0.1277	0.0403	-0.047	0.1235	0.0212	-0.0471	0.0373	-0.0265	0.1065	0.1858	-0.0666	0.0254	0.1324	0.0298	0.0404	3.1371	10.9532	45.198
2	0.6469	-0.0928	-0.6255	0.3988	0.467	1.1254	0.073	-0.025	0.1147	-0.0197	0.1277	-0.1909	0.0084	0.0323	-0.2007	0.061	-0.0568	0.0749	0.1299	-0.091	0.1756	34.2162	22.9273	5.7567
3	0.627	-0.0679	-0.1154	1.3201	-0.2073	0.203	0.0922	0.0759	-0.0423	0.1938	-0.1648	-0.0388	-0.1167	0.003	0.0726	0.1301	-0.0716	-0.0009	0.1196	-0.0418	0.0511	-25.928	51.7377	31.6957

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	26 - 601
2	X-RAY DIFFRACTION	2	B	26 - 601
3	X-RAY DIFFRACTION	3	C	26 - 601

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