PDB-5zwx: Crystal structure of Raphanus sativus AGDP1 AGD12 in complex with...

ID or keywords:

Entry

Database: PDB / ID: 5zwx

Title

Crystal structure of Raphanus sativus AGDP1 AGD12 in complex with an H3K9me2 peptide

Components

DUF724 domain-containing protein 6-like
H3(1-15)K9me2 peptide

Keywords

GENE REGULATION / AGENET domain / AGDP1 /

epigenetics /

H3K9me2

Function / homology

Function and homology information

chromocenter /

plastid / structural constituent of chromatin /

nucleosome / protein heterodimerization activity /

DNA binding / extracellular region /

nucleus /

plasma membrane /

cytosol
Similarity search - Function

Biological species

Raphanus sativus (radish)

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.9 Å

Authors

Du, X. / Du, J.

Funding support

China, 1items

Citation

Journal: Nat Commun / Year: 2018
Title: Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin
Authors: Zhang, C. / Du, X. / Tang, K. / Yang, Z. / Pan, L. / Zhu, P. / Luo, J. / Jiang, Y. / Zhang, H. / Wan, H. / Wang, X. / Wu, F. / Tao, W.A. / He, X.J. / Zhang, H. / Bressan, R.A. / Du, J. / Zhu, J.K.

History

Deposition	May 17, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 14, 2018	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5zwx.cif.gz	148 KB	Display	PDBx/mmCIF format
PDB format	pdb5zwx.ent.gz	123.1 KB	Display	PDB format
PDBx/mmJSON format	5zwx.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/zw/5zwx ftp://data.pdbj.org/pub/pdb/validation_reports/zw/5zwx	HTTPS FTP

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Related structure data

Related structure data	5zwzC C: citing same article (ref.)
Similar structure data	1zs7-d 4gix-d 1jaj-d 1aw7-4 2cx1-d 3tr3-2 1ohz-d 3o13-d 3fau-2 5aq0-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#7 - Jul 2000 Nucleosome similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: DUF724 domain-containing protein 6-like

P: H3(1-15)K9me2 peptide

B: DUF724 domain-containing protein 6-like

Q: H3(1-15)K9me2 peptide

40.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DUF724 domain-containing protein 6-like

P: H3(1-15)K9me2 peptide

defined by author&software
Evidence: isothermal titration calorimetry
20.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DUF724 domain-containing protein 6-like

Q: H3(1-15)K9me2 peptide

defined by author&software
Evidence: isothermal titration calorimetry
20.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	47.653, 54.981, 83.576
Angle α, β, γ (deg.)	90.00, 99.72, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	DUF724 domain-containing protein 6-like / AGDP1 AGD12 cassette Mass: 18633.326 Da / Num. of mol.: 2 / Mutation: L54M, L135M, L140M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Raphanus sativus (radish) / Plasmid: pMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: A0A493R6M0*PLUS
#2: Protein/peptide	H3(1-15)K9me2 peptide Mass: 1592.843 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	Sequence of entity 1 has been deposited to NCBI with accession number XP_018485729. Residues ...Sequence of entity 1 has been deposited to NCBI with accession number XP_018485729. Residues L54M/L135M/L140M represent mutations.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.21 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 15% PEG 20000, 0.1M MES, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9778 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 33643 / % possible obs: 99.7 % / Redundancy: 6.7 % / R_merge(I) obs: 0.082 / Net I/σ(I): 21.5
Reflection shell	Resolution: 1.9→1.97 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.567 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3346 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.9→41.188 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 23.95

	R_factor	Num. reflection	% reflection
R_free	0.2113	1705	5.07 %
R_work	0.1819	-	-
obs	0.1834	33643	99.66 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→41.188 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2566	0	0	248	2814

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	2626
X-RAY DIFFRACTION	f_angle_d	1.422	3540
X-RAY DIFFRACTION	f_dihedral_angle_d	15.559	1000
X-RAY DIFFRACTION	f_chiral_restr	0.065	362
X-RAY DIFFRACTION	f_plane_restr	0.006	462

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 (%)
1.9001-1.9272	0.3178	138	0.2519	2571	X-RAY DIFFRACTION	100
1.9272-1.956	0.2292	125	0.2462	2570	X-RAY DIFFRACTION	99
1.956-1.9865	0.3348	143	0.2337	2606	X-RAY DIFFRACTION	100
1.9865-2.0191	0.2939	166	0.2266	2570	X-RAY DIFFRACTION	100
2.0191-2.0539	0.2498	161	0.2211	2559	X-RAY DIFFRACTION	100
2.0539-2.0913	0.2363	116	0.2153	2646	X-RAY DIFFRACTION	100
2.0913-2.1315	0.2673	133	0.2056	2612	X-RAY DIFFRACTION	100
2.1315-2.175	0.2254	135	0.209	2612	X-RAY DIFFRACTION	100
2.175-2.2223	0.2139	130	0.2048	2603	X-RAY DIFFRACTION	100
2.2223-2.274	0.2123	144	0.198	2651	X-RAY DIFFRACTION	100
2.274-2.3308	0.3284	100	0.1975	2566	X-RAY DIFFRACTION	100
2.3308-2.3939	0.2416	162	0.1963	2638	X-RAY DIFFRACTION	100
2.3939-2.4643	0.2165	130	0.1979	2565	X-RAY DIFFRACTION	100
2.4643-2.5438	0.2487	138	0.1891	2583	X-RAY DIFFRACTION	99
2.5438-2.6347	0.2102	140	0.1988	2621	X-RAY DIFFRACTION	100
2.6347-2.7402	0.197	174	0.1857	2548	X-RAY DIFFRACTION	100
2.7402-2.8649	0.2139	119	0.1889	2619	X-RAY DIFFRACTION	100
2.8649-3.0159	0.2145	133	0.1875	2631	X-RAY DIFFRACTION	100
3.0159-3.2048	0.1975	141	0.1778	2618	X-RAY DIFFRACTION	100
3.2048-3.4521	0.1923	152	0.1667	2594	X-RAY DIFFRACTION	100
3.4521-3.7993	0.1967	129	0.1623	2569	X-RAY DIFFRACTION	100
3.7993-4.3485	0.1988	136	0.1492	2611	X-RAY DIFFRACTION	100
4.3485-5.4766	0.1645	125	0.1555	2613	X-RAY DIFFRACTION	99
5.4766-41.1974	0.2123	158	0.1938	2533	X-RAY DIFFRACTION	99

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	7.956	2.0319	-1.4182	3.5626	-1.3167	2.3298	-0.6247	0.5696	0.5223	-1.1746	0.764	0.2124	0.4584	-0.6333	-0.1334	0.5035	-0.0909	-0.1007	0.4805	0.078	0.3883	10.4963	36.4198	-12.2428
2	9.1174	3.5443	3.905	8.6961	1.1364	2.3907	-0.3543	0.2667	0.6203	0.7517	0.4603	0.1578	-0.735	-0.0607	-0.0362	0.3898	-0.0404	-0.0322	0.3153	0.0733	0.2546	13.7305	34.0153	2.7465
3	2.8948	-2.2841	1.5256	2.9351	-2.9872	6.7379	-0.2389	0.2133	-0.0595	0.1069	0.4409	0.3624	-0.1174	-0.57	-0.1497	0.25	-0.0019	-0.0087	0.3183	0.0854	0.2686	12.2894	32.5591	4.2885
4	3.5547	-0.7628	-0.1706	4.0168	1.0717	3.4352	-0.296	-0.1084	0.3747	-0.4736	0.5766	0.8143	-0.3975	-1.1698	-0.0504	0.1895	0.1239	-0.0154	0.5803	0.2076	0.4248	5.8868	38.1525	1.3892
5	1.3487	-2.8155	1.6288	2.0047	1.1515	7.1535	0.2922	0.6215	-1.8943	0.1197	0.5536	0.2442	2.7381	1.1197	-0.6026	1.3051	-0.1314	-0.1557	0.5419	-0.0154	1.0807	15.92	11.6496	-3.0527
6	2.4647	1.3488	0.0258	5.8086	-4.5926	4.1984	0.1957	1.0759	-0.7567	-1.8053	0.1567	0.9141	1.806	0.0571	-0.4844	0.7412	0.1036	-0.0918	0.452	-0.1354	0.3318	25.6481	11.2437	6.2236
7	7.2565	-3.4663	0.1965	5.4632	1.1385	3.5602	-0.3219	0.0215	-0.0707	0.2006	0.3388	-0.0464	0.4001	0.0027	-0.02	0.2539	-0.0333	0.0167	0.2166	-0.0041	0.1869	19.5412	20.7633	11.2348
8	7.7613	0.9774	0.2894	3.0413	-0.0482	7.9062	0.3412	-0.1546	-0.4378	0.0927	-0.2574	-0.9325	1.0514	-0.1133	0.039	0.3486	0.0372	0.0031	0.3151	0.0035	0.1933	23.3544	19.6058	15.1988
9	2.7591	-0.3666	0.3685	3.2418	0.0362	5.9658	0.0497	0.0319	-0.194	0.0591	0.1081	0.0294	0.7961	-0.2269	-0.1087	0.2895	-0.0204	0.0054	0.1813	-0.0042	0.2425	18.0957	17.188	12.6374
10	5.5971	-2.0702	0.9399	2.2731	-4.0221	9.5185	0.0174	0.752	-0.2787	-1.2323	0.0835	-0.3212	1.039	0.432	-0.05	0.5748	-0.0259	0.0801	0.3992	-0.0032	0.3066	21.3622	23.9464	-6.5205
11	2.1243	-1.1387	2.1856	4.596	-1.9252	5.1318	-0.5734	-0.3128	0.3549	0.4927	0.4493	0.187	-0.5411	-0.6795	-0.0004	0.3849	0.0914	0.0292	0.3401	0.065	0.3035	10.6106	34.2088	15.6737
12	5.2211	-0.5393	2.4576	9.8638	-1.9114	5.0461	-0.1513	-0.473	-1.059	0.8894	0.5658	-0.0173	-0.2362	-0.8561	-0.2487	0.4166	0.0402	0.1161	0.5062	0.0592	0.4407	0.0741	10.021	48.2189
13	2.3094	-3.4603	-1.8463	7.1227	0.6746	7.1423	-0.31	0.2395	-0.4456	-0.556	0.1623	-0.088	0.6224	-0.1609	0.0772	0.3583	0.0158	0.0848	0.2449	0.015	0.3574	8.1443	12.4415	35.326
14	4.546	2.2964	-1.6365	5.1416	-1.6723	6.4491	-0.1822	-0.2848	0.2404	-0.0956	0.2586	0.1019	0.1082	-0.5804	-0.1137	0.2485	0.0186	-0.0136	0.2504	0.0382	0.204	7.3866	13.9806	33.213
15	3.6399	-0.1047	0.275	3.8105	0.267	2.8096	0.125	0.1208	-0.5165	0.1267	0.1858	0.5755	0.6105	-0.8721	-0.2245	0.2733	-0.0848	-0.0106	0.4187	0.071	0.3573	0.2023	8.3169	33.8013
16	4.0469	4.0356	-2.3946	4.2275	-2.0653	1.6366	1.1956	-0.6848	2.3235	0.738	0.0365	1.6724	-1.5675	-0.0253	-0.2025	0.9101	0.065	0.2334	0.5195	-0.108	0.7881	12.9569	34.8443	39.0113
17	7.3952	3.4795	0.6829	4.8779	1.9789	3.067	-0.2299	-0.0004	0.1843	-0.1319	0.2385	0.0412	-0.3869	0.0282	-0.1811	0.2938	0.0833	-0.0127	0.2027	-0.0018	0.1803	16.516	25.6819	29.2113
18	7.0145	-1.4364	-0.1309	3.7051	-2.0352	6.8435	0.5517	0.385	0.6374	0.0101	-0.5029	-1.2052	-0.8889	0.0669	-0.0576	0.4002	0.0052	0.0261	0.2755	-0.0038	0.1961	21.3331	26.9066	26.7588
19	2.5875	0.1835	-1.8859	3.0228	0.2513	3.141	0.3764	0.099	0.3723	-0.0072	0.0123	0.084	-0.764	-0.2967	-0.3005	0.349	0.0681	0.0031	0.1988	0.0058	0.255	15.5962	29.2762	27.4224
20	5.9207	2.8858	-2.8213	1.4849	-1.2241	7.5682	0.0644	-0.5965	0.2811	1.0461	0.0559	-0.0759	-0.4512	0.4019	-0.1727	0.6287	0.0505	-0.008	0.338	0.0108	0.2775	12.3156	22.4683	46.5952
21	2.595	1.8059	3.1562	3.594	-0.3929	7.2636	-0.2788	0.1821	-0.3606	-0.4683	0.2686	0.0861	0.3329	-0.591	0.0031	0.2794	-0.0208	0.0067	0.3147	0.0084	0.2872	9.7011	12.3666	21.942

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 26 through 37 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 45 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 46 through 59 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 60 through 98 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 99 through 109 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 110 through 116 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 117 through 135 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 136 through 148 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 149 through 160 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 161 through 173 )
11	X-RAY DIFFRACTION	11	chain 'P' and (resid 1 through 10 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 26 through 37 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 38 through 45 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 46 through 59 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 60 through 98 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 99 through 116 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 117 through 135 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 136 through 148 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 149 through 160 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 161 through 173 )
21	X-RAY DIFFRACTION	21	chain 'Q' and (resid 1 through 10 )

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