PDB-5xpc: Crystal Structure of Drep4 CIDE domain

ID or keywords:

Entry

Database: PDB / ID: 5xpc

Title

Crystal Structure of Drep4 CIDE domain

Components

DNAation factor-related protein 4

Keywords

APOPTOSIS / Energy metabolism / DNA Fragmentation Factor / drep4 / CIDE

Function / homology

Function and homology information

Apoptosis induced DNA fragmentation / DNA nuclease activity / apoptotic DNA fragmentation / nucleosome binding / DNA endonuclease activity / nucleus / cytoplasm
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.902 Å

Authors

Park, H.H. / Jeong, J.H.

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: CIDE domains form functionally important higher-order assemblies for DNA fragmentation.
Authors: Choi, J.Y. / Qiao, Q. / Hong, S.H. / Kim, C.M. / Jeong, J.H. / Kim, Y.G. / Jung, Y.K. / Wu, H. / Park, H.H.

History

Deposition	Jun 1, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 26, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2019	Group: Data collection / Category: reflns / reflns_shell Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5xpc.cif.gz	188.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5xpc.ent.gz	153.3 KB	Display	PDB format
PDBx/mmJSON format	5xpc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xp/5xpc ftp://data.pdbj.org/pub/pdb/validation_reports/xp/5xpc	HTTPS FTP

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Related structure data

Related structure data	4d2kC 5xpbS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2bva-d 6xxq-d 5uxv-d 5ygr-2 1a3a-d 6kmv-15 3fdm-d 2xnj-d 1jke-5 3ag9-d Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#56 - Aug 2004 Caspases similarity (7)

Deposited unit

A: DNAation factor-related protein 4

B: DNAation factor-related protein 4

C: DNAation factor-related protein 4

D: DNAation factor-related protein 4

E: DNAation factor-related protein 4

hetero molecules

57.2 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	53.081, 76.588, 174.597
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	DNAation factor-related protein 4 / Drep4 Mass: 11216.620 Da / Num. of mol.: 5 / Fragment: UNP RESIDUES 39-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Drep4, Drep-4, drep4, Rep4, CG9414, Dmel_CG9414 / Plasmid: pOKD / Details (production host): non-commercial / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9V3H0
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.16 Å³/Da / Density % sol: 61.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M tris-hydrochloride pH 8.5, 20 mM ammonium phosphate

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2014 / Details: mirrors
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 56853 / % possible obs: 99.98 % / Redundancy: 7.2 % / R_sym value: 0.084 / Net I/σ(I): 0.352
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.0366 / Num. unique obs: 5578 / R_sym value: 0.706 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155)	refinement
PHENIX	(1.10.1_2155)	data reduction
HKL-2000		data scaling
PHENIX	(1.10.1_2155)	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5XPB

5xpb

Resolution: 1.902→35.068 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.45

	R_factor	Num. reflection	% reflection
R_free	0.2139	1945	3.54 %
R_work	0.1863	-	-
obs	0.1872	54880	96.5 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.902→35.068 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3391	0	72	185	3648

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3523
X-RAY DIFFRACTION	f_angle_d	0.805	4732
X-RAY DIFFRACTION	f_dihedral_angle_d	12.924	2135
X-RAY DIFFRACTION	f_chiral_restr	0.056	518
X-RAY DIFFRACTION	f_plane_restr	0.005	603

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9016-1.9492	0.2733	127	0.2241	3374	X-RAY DIFFRACTION	88
1.9492-2.0019	0.236	128	0.2013	3482	X-RAY DIFFRACTION	90
2.0019-2.0608	0.2531	128	0.1958	3602	X-RAY DIFFRACTION	93
2.0608-2.1273	0.2296	137	0.1887	3724	X-RAY DIFFRACTION	95
2.1273-2.2033	0.2164	135	0.1867	3688	X-RAY DIFFRACTION	96
2.2033-2.2915	0.2112	140	0.1816	3721	X-RAY DIFFRACTION	96
2.2915-2.3958	0.2403	139	0.1861	3781	X-RAY DIFFRACTION	97
2.3958-2.522	0.2295	140	0.1997	3792	X-RAY DIFFRACTION	97
2.522-2.68	0.2443	143	0.1967	3849	X-RAY DIFFRACTION	99
2.68-2.8868	0.198	142	0.2031	3865	X-RAY DIFFRACTION	99
2.8868-3.1772	0.2264	143	0.2089	3932	X-RAY DIFFRACTION	100
3.1772-3.6365	0.2291	144	0.2022	3949	X-RAY DIFFRACTION	100
3.6365-4.58	0.181	147	0.1526	3993	X-RAY DIFFRACTION	100
4.58-35.0744	0.1939	152	0.1748	4183	X-RAY DIFFRACTION	100

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	3.149	0.2048	-0.1824	1.6004	0.7852	2.1844	0.0316	-0.2375	-0.222	-0.0113	-0.067	-0.0071	0.1989	-0.0754	0.0104	0.1947	0.0209	-0.0011	0.2113	-0.0203	0.1642	11.2307	27.2217	99.5918
2	3.5604	-0.4111	1.3089	6.6109	0.1735	2.2121	-0.1687	-0.1718	-0.3309	0.5141	0.0547	0.1437	0.6621	-0.58	0.0259	0.3444	-0.0921	0.0346	0.2953	-0.0156	0.2349	5.631	23.2733	105.3819
3	3.1831	0.8751	0.4157	4.3685	-0.0112	3.64	0.2115	-0.2188	-0.2244	0.3276	-0.077	0.5542	0.8149	0.0255	0.0176	0.439	0.0118	-0.065	0.2827	0.0061	0.3078	14.1247	22.4038	109.1541
4	0.7589	0.6459	-0.0428	1.6313	0.4954	1.6829	0.0746	-0.0339	0.0728	0.1471	-0.0879	0.0577	-0.0056	-0.0572	-0.0059	0.2688	-0.0041	-0.0452	0.2506	-0.0231	0.2202	12.033	35.6244	107.5089
5	2.2042	0.3488	0.2604	3.0387	-1.2065	1.2276	0.2936	-0.5368	-0.1663	0.5654	-0.181	-0.1123	-0.0126	0.3123	0.0397	0.3856	0.0217	-0.0823	0.4202	-0.0153	0.2706	19.937	26.4518	108.0684
6	7.6357	1.4585	-2.3366	0.9267	-0.1287	0.8671	0.3996	-0.0336	-0.042	0.1054	0.118	-1.6257	0.2756	0.9705	0.0366	0.533	0.0806	-0.0588	0.641	-0.0477	0.7531	31.5752	33.3118	102.7213
7	1.7179	0.7271	-0.058	3.3293	0.3693	2.5934	-0.0335	-0.018	-0.2097	0.1492	-0.0763	-0.0922	0.1674	-0.0405	0.0017	0.2664	0.019	-0.0429	0.1906	-0.0187	0.1727	15.7011	39.773	116.7777
8	2.7799	0.5215	1.8773	5.9241	-2.6663	2.8809	0.0962	-0.3868	-0.163	0.3275	-0.0202	0.4023	0.3317	-0.2607	-0.0329	0.3138	-0.0315	-0.0146	0.2449	-0.025	0.2129	10.8293	39.9047	123.5009
9	0.7177	-0.0222	0.0153	1.9411	-0.2961	0.8125	-0.0218	0.0041	0.044	0.296	-0.0096	-0.0355	0.0888	0.0497	-0.0114	0.3294	0.0012	-0.0583	0.2238	-0.0133	0.2153	18.3386	46.8806	121.1578
10	5.7684	1.3909	-5.6724	0.7832	-1.9419	6.3348	0.8896	-0.9961	1.1944	0.9646	-0.1713	-0.7429	-0.8162	1.1069	-0.1453	0.5065	-0.1048	-0.0568	0.4806	-0.0723	0.3896	27.3599	45.1135	126.4348
11	4.088	-1.3277	0.6867	0.4452	-0.0919	1.0799	-0.3369	0.5968	-0.7633	-0.3285	0.0183	-0.9934	0.5937	0.3848	0.079	0.4683	0.0585	0.0362	0.5394	-0.0898	0.7946	36.3569	39.4963	115.0255
12	2.6494	0.5295	0.5983	2.6751	-0.0718	2.9653	-0.0638	0.3456	-0.2037	0.1879	0.1398	0.2045	-0.1743	0.0955	-0.0133	0.3316	-0.0131	-0.0812	0.1946	0.0183	0.2431	17.1808	61.186	117.741
13	3.965	0.2738	0.2909	3.1046	-0.7737	1.2558	0.1988	-0.4306	-0.207	0.5992	-0.1398	-0.2747	0.0898	0.0061	-0.0144	0.3755	0.0213	-0.0747	0.232	0.021	0.2285	24.3225	58.9496	125.6021
14	3.3248	2.1341	0.8594	2.2692	-1.5344	6.9209	0.2399	-0.3132	0.1787	0.5215	-0.4225	0.185	-0.0683	-0.1782	-0.0598	0.349	-0.0284	0.0539	0.257	0.007	0.238	16.0792	64.5576	127.3277
15	1.8741	1.0619	-0.9083	2.34	-2.0888	3.3853	0.387	-0.143	-0.1132	0.7251	-0.0813	-0.0093	-0.3938	-0.125	-0.0503	0.546	-0.0229	-0.0557	0.2876	0.0413	0.2513	24.3711	67.6717	129.2866
16	0.6524	0.9026	-0.0467	1.8672	-0.3179	1.3344	0.064	0.1161	-0.046	0.185	0.094	-0.0581	0.0225	-0.0099	-0.0276	0.3347	0.0141	-0.0251	0.2188	0.0109	0.1931	25.7494	68.5685	119.4254
17	5.2993	-1.6139	1.9588	4.4563	-3.1605	5.2745	-0.1828	0.1414	-0.7717	0.128	-0.2828	-1.4475	0.1654	0.8387	0.0382	0.4424	0.0972	-0.1209	0.4059	-0.0141	0.6405	41.4196	58.7531	121.5037
18	1.539	0.442	-0.593	2.6318	-1.0419	2.2561	0.1138	-0.0186	0.0317	0.242	0.0305	0.021	-0.002	0.0547	-0.0273	0.2847	0.0211	-0.0399	0.2297	0.0454	0.191	27.4525	78.7698	114.0308
19	2.8519	2.1512	-0.2023	2.724	1.8021	7.128	0.0351	-0.2005	0.2406	0.5033	0.2777	0.3776	-0.5899	-0.4182	-0.0169	0.3871	0.0871	0.0492	0.2514	0.0549	0.2166	22.1362	85.4978	115.1343
20	1.5071	0.0801	0.1962	1.4941	-1.1367	2.2072	-0.0445	-0.0468	0.0851	0.2112	0.016	-0.0113	-0.239	-0.0794	-0.0184	0.2488	0.0172	-0.001	0.2159	0.0156	0.1752	29.6986	84.7728	107.9739
21	5.9202	-5.6217	-2.6773	7.4209	3.068	1.4695	0.2411	-0.0593	0.6877	-0.1005	-0.2288	-1.2172	-0.6864	0.6101	-0.02	0.4167	-0.0208	-0.0323	0.3146	0.0451	0.3648	38.7728	89.3123	110.6878
22	3.9004	2.2172	2.3333	1.7545	1.4488	1.4178	-0.0693	-0.3543	-0.4282	0.6696	0.0873	-0.7051	0.3167	0.796	-0.1382	0.4176	0.1363	-0.0584	0.6032	0.1047	0.5678	47.6866	76.9657	113.2242
23	3.8385	1.5516	-0.3717	4.1458	0.1406	2.1134	-0.0247	-0.0562	-0.3853	0.1086	-0.0127	0.0406	-0.0554	-0.3901	-0.0271	0.2334	-0.0241	-0.0122	0.2295	0.0045	0.1825	27.5273	85.3858	92.803
24	4.876	-0.5346	-3.1218	4.0844	1.7512	2.4938	0.0935	-1.3266	0.2527	0.1316	-0.0961	-0.0156	-0.6531	0.4273	-0.1671	0.3135	-0.0952	-0.0516	0.4686	-0.0377	0.2105	42.6417	94.2762	98.7085
25	2.8862	0.6399	1.0933	2.6603	0.1762	3.1107	0.0025	0.0347	0.0185	0.1032	-0.0138	-0.0091	-0.1994	0.002	0.0049	0.19	0.0341	0.0001	0.216	-0.0116	0.1752	28.2114	93.0648	94.3765
26	1.8734	0.9428	-0.0089	1.7051	0.3664	4.3164	0.2074	-0.0041	0.1486	0.0406	-0.1766	0.0606	-0.3434	-0.0468	-0.0398	0.213	-0.0066	0.0217	0.1821	-0.011	0.2166	36.6532	94.3623	87.3186
27	0.8532	0.0562	-0.4923	2.1061	-0.0046	1.7907	-0.0161	0.0787	-0.1732	0.0415	-0.023	-0.0608	0.0322	-0.1195	-0.0378	0.1992	-0.0044	0.0022	0.2011	-0.0065	0.2138	32.6931	86.1915	87.6265
28	7.9436	-4.2474	0.2476	6.8049	0.1143	2.913	0.4192	0.1289	0.1801	-0.4813	-0.2244	-0.2105	0.0406	0.4544	-0.0031	0.1686	-0.0466	-0.0204	0.2184	-0.0128	0.1882	44.1048	95.766	86.7907
29	6.3904	-1.6644	1.1025	2.862	2.5264	4.101	-0.1485	-1.0891	-0.4916	0.7222	-0.1476	-0.5513	0.3405	0.7952	-0.0471	0.4015	0.0469	-0.1467	0.6497	0.1483	0.5007	52.4111	86.3789	95.658

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 45 through 67 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 68 through 78 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 79 through 88 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 89 through 108 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 109 through 121 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 122 through 129 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 44 through 67 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 68 through 78 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 79 through 113 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 114 through 121 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 122 through 131 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 45 through 53 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 54 through 67 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 68 through 78 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 79 through 88 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 89 through 121 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 122 through 130 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 45 through 67 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 68 through 78 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 79 through 113 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 114 through 121 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 122 through 131 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 44 through 53 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 54 through 59 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 60 through 78 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 79 through 97 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 98 through 113 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 114 through 121 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 122 through 130 )

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