PDB-4iup: crystal structure of Se-substituted arabidopsis thaliana SHH1 SAW...

ID or keywords:

Entry

Database: PDB / ID: 4iup

Title

crystal structure of Se-substituted arabidopsis thaliana SHH1 SAWADEE domain L200M/L218M mutant

Components

SAWADEE HOMEODOMAIN HOMOLOG 1

Keywords

GENE REGULATION / tandem tudor / zinc finger / mediate interaction / histone / DNA BINDING PROTEIN

Function / homology

Function and homology information

regulatory ncRNA-mediated gene silencing / DNA methylation-dependent constitutive heterochromatin formation / chromatin binding / nucleus / metal ion binding
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.9 Å

Authors

Du, J. / Patel, D.J.

Citation

Journal: Nature / Year: 2013
Title: Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.
Authors: Law, J.A. / Du, J. / Hale, C.J. / Feng, S. / Krajewski, K. / Palanca, A.M. / Strahl, B.D. / Patel, D.J. / Jacobsen, S.E.

History

Deposition	Jan 21, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 1, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2013	Group: Database references
Revision 1.2	Jul 10, 2013	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4iup.cif.gz	128.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4iup.ent.gz	107 KB	Display	PDB format
PDBx/mmJSON format	4iup.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4iup_validation.pdf.gz	864.8 KB	Display	wwPDB validaton report
Full document	4iup_full_validation.pdf.gz	867.1 KB	Display
Data in XML	4iup_validation.xml.gz	18 KB	Display
Data in CIF	4iup_validation.cif.gz	26.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iu/4iup ftp://data.pdbj.org/pub/pdb/validation_reports/iu/4iup	HTTPS FTP

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Related structure data

Related structure data	4iuqC 4iurC 4iutC 4iuuC 4iuvC C: citing same article (ref.)
Similar structure data	4iuu-1 4iuq-2 4iuq-1 4iuv-1 2xl4-d 4iut-2 4iur-1 4iuu-2 3a5p-2 4cih-2 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	#87 - Mar 2007 Zinc Fingers similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1)

Deposited unit

A: SAWADEE HOMEODOMAIN HOMOLOG 1

B: SAWADEE HOMEODOMAIN HOMOLOG 1

hetero molecules

33.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: SAWADEE HOMEODOMAIN HOMOLOG 1

hetero molecules

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

2

B: SAWADEE HOMEODOMAIN HOMOLOG 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.293, 56.733, 59.299
Angle α, β, γ (deg.)	90.00, 93.36, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	SAWADEE HOMEODOMAIN HOMOLOG 1 / Uncharacterized protein Mass: 15910.512 Da / Num. of mol.: 2 / Fragment: SHH1 SAWADEE domain (unp residues 125-258) / Mutation: L200M, L218M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F9L1.16, At1g15215, AT1G15215 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9XI47
#2: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-CVM / CYMAL-4 / 4-CYCLOHEXYLBUTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE Mass: 480.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₂H₄₀O₁₁
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.81 Å³/Da / Density % sol: 56.26 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl- -D-Maltoside 7K, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2011
Radiation	Monochromator: SI MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.9→30 Å / Num. all: 54961 / Num. obs: 54961 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / R_merge(I) obs: 0.126 / R_sym value: 0.126 / Net I/σ(I): 12.2
Reflection shell	Resolution: 1.9→1.97 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.521 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5503 / R_sym value: 0.521 / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.7_650)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.9→29.599 Å / SU ML: 0.19 / σ(F): 0.61 / Phase error: 17.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1944	1412	5.02 %	RANDOM
R_work	0.1717	-	-	-
obs	0.1729	54536	99.88 %	-
all	-	57273	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 32.85 Å² / k_sol: 0.341 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.9906 Å²	0 Å²	-0.4351 Å²
2-	-	3.9355 Å²	-0 Å²
3-	-	-	-0.9449 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→29.599 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2148	0	54	443	2645

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	2248
X-RAY DIFFRACTION	f_angle_d	1.187	3026
X-RAY DIFFRACTION	f_dihedral_angle_d	14.523	841
X-RAY DIFFRACTION	f_chiral_restr	0.092	325
X-RAY DIFFRACTION	f_plane_restr	0.004	391

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 (%)
1.9-1.9328	0.2342	123	0.2222	2557	X-RAY DIFFRACTION	100
1.9328-1.9679	0.2301	126	0.2072	2613	X-RAY DIFFRACTION	100
1.9679-2.0058	0.2271	131	0.1923	2585	X-RAY DIFFRACTION	100
2.0058-2.0467	0.2324	157	0.1881	2627	X-RAY DIFFRACTION	100
2.0467-2.0912	0.2296	154	0.1842	2525	X-RAY DIFFRACTION	100
2.0912-2.1398	0.2098	134	0.184	2565	X-RAY DIFFRACTION	100
2.1398-2.1933	0.2307	167	0.1653	2600	X-RAY DIFFRACTION	100
2.1933-2.2526	0.1931	130	0.1613	2580	X-RAY DIFFRACTION	100
2.2526-2.3189	0.1871	147	0.158	2615	X-RAY DIFFRACTION	100
2.3189-2.3937	0.195	116	0.1658	2593	X-RAY DIFFRACTION	100
2.3937-2.4792	0.2457	125	0.1835	2615	X-RAY DIFFRACTION	100
2.4792-2.5784	0.1961	126	0.1795	2622	X-RAY DIFFRACTION	100
2.5784-2.6957	0.1806	149	0.1735	2591	X-RAY DIFFRACTION	100
2.6957-2.8377	0.207	125	0.17	2612	X-RAY DIFFRACTION	100
2.8377-3.0153	0.1716	121	0.1692	2571	X-RAY DIFFRACTION	100
3.0153-3.2478	0.1834	150	0.1726	2565	X-RAY DIFFRACTION	100
3.2478-3.5742	0.195	151	0.1605	2608	X-RAY DIFFRACTION	100
3.5742-4.0902	0.1756	112	0.156	2611	X-RAY DIFFRACTION	100
4.0902-5.1488	0.1538	151	0.1425	2587	X-RAY DIFFRACTION	100
5.1488-29.6023	0.1908	142	0.1983	2557	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	0.1136	-0.0178	-0.0454	0.1064	0.1714	0.316	0.0756	-0.0891	0.1319	0.0505	-0.0537	-0.0055	0.0023	-0.0239	-0.0203	0.076	-0.008	0.0015	0.0926	-0.0327	0.097	27.8673	52.2239	56.2974
2	0.034	0.0362	-0.0127	0.1082	0.1617	0.4863	0.103	0.0389	-0.0433	0.0074	0.0144	-0.0789	0.1239	0.0049	0.0143	0.0532	0.0167	-0.0054	0.0532	-0.0219	0.0687	32.2408	44.3354	50.4244
3	0.4502	-0.0883	-0.2716	0.1944	0.0313	0.4748	0.0546	0.1262	0.0514	0.0382	-0.0396	-0.1174	-0.0214	0.0152	-0.0035	0.0935	0.0068	0.0316	0.1095	-0.0089	0.1346	46.9765	52.4002	51.07
4	0.1092	-0.0344	-0.0249	0.0535	0.0546	0.0593	0.081	0.0125	-0.1011	0.0068	0.0125	0.0135	0.06	0.0046	0.1061	0.0687	0.0713	-0.0403	-0.1063	-0.0346	0.1487	37.6878	44.7936	55.6744
5	0.0924	0.057	-0.0449	0.0355	-0.0345	0.0521	0.0088	-0.0043	-0.0173	-0.0025	-0.0399	0.0649	-0.127	-0.0237	-0.0371	0.0629	0.0272	0.0043	0.018	-0.0437	0.1034	35.4963	51.2008	50.0129
6	0.0108	0.0013	0.0295	0.0851	-0.014	0.0978	0.0469	-0.0216	0.0076	0.0233	0.0248	-0.0056	-0.0046	-0.0207	0.007	0.0681	-0.0025	0.0132	0.062	-0.0015	0.0918	16.7941	50.5545	53.2221
7	0.1354	-0.0245	-0.1689	0.1209	-0.0149	0.6279	-0.0533	-0.0494	0.0857	-0.0398	0.0354	-0.0465	-0.0199	-0.1234	-0.0015	0.0742	0.0242	0.0139	0.0769	0.0029	0.0804	10.4232	55.092	45.16
8	0.0321	0.0546	-0.0332	0.2447	0.0421	0.1216	-0.0301	0.047	0.0589	-0.0023	0.0061	0.0498	0.1161	-0.0335	-0.0105	0.1084	0.0031	0.0046	0.0303	-0.0127	0.0664	20.9701	40.7233	42.5584
9	0.5755	0.1876	-0.0493	0.2495	0.0018	0.1421	0.0109	0.1997	0.0993	-0.064	0.0566	-0.0198	0.0551	-0.0723	0.096	0.0902	0.0189	0.0172	0.0436	0.0417	0.024	18.642	46.3446	39.729
10	0.0503	0.0829	-0.0539	0.3508	0.0473	0.1917	-0.0121	0.0092	-0.0388	-0.0728	-0.0254	0.1393	0.1239	-0.0629	-0.058	0.0619	0.0249	0.0054	0.0939	0.028	0.0697	7.027	47.3102	42.646
11	0.0479	-0.0283	0.0737	0.0418	-0.0428	0.1167	-0.0072	0.0352	-0.0364	-0.1222	-0.0412	0.0711	0.024	0.0535	0.006	0.0833	0.0227	-0.0093	0.0755	0.0077	0.057	20.687	44.3078	35.5207
12	0.147	0.1012	0.0544	0.0838	-0.0047	0.1508	-0.0005	0.0037	-0.0326	-0.0136	-0.0319	0.0614	0.0514	-0.0428	0.0045	0.0544	0.0135	-0.0125	0.0504	-0.0009	0.0777	16.5864	50.5274	48.1147
13	0.0141	0.024	0.0547	0.1062	0.0099	0.2583	-0.0094	0.1196	-0.0183	-0.011	0.046	-0.0568	0.0595	0.0579	0.0125	0.056	-0.0163	-0.0037	0.0911	0.0167	0.0713	2.1657	25.1668	46.9412
14	0.5132	0.2073	-0.1116	0.1515	-0.1103	0.1468	-0.0441	0.1048	-0.1109	-0.054	0.0434	-0.0765	-0.054	0.0407	-0.0025	0.0697	-0.0111	0.0161	0.082	0.0153	0.0828	13.3337	28.251	49.109
15	0.1244	-0.0835	0.1066	0.2445	0.0344	0.3038	-0.0156	-0.0556	0.0682	-0.0022	-0.0412	-0.0147	-0.0211	-0.1224	0.0289	0.0787	-0.0107	0.0067	0.1019	-0.0008	0.07	-6.7426	26.9334	47.3537
16	0.0102	0.0167	0.0067	0.1171	0.0224	0.0067	-0.0697	0.1659	0.0091	-0.0704	-0.0533	0.0766	0.0356	-0.0323	0.0014	0.1271	-0.0028	-0.0075	0.2181	-0.0308	0.0619	-6.2243	26.3554	33.7492
17	0.3147	-0.1842	0.1958	0.296	-0.3201	0.3468	-0.0632	0.0877	0.1338	-0.0201	-0.0673	0.0242	-0.0887	0.0618	-0.0454	0.0925	-0.0033	-0.0257	0.1033	-0.0275	0.0747	-10.8943	30.1196	36.5821
18	0.0108	0.037	0.0304	0.1139	0.0905	0.0706	-0.0089	0.0044	-0.0438	-0.0035	-0.0441	0.0389	0.0415	-0.074	-0.0336	0.0619	-0.0557	-0.0087	0.0111	-0.1989	0.061	-24.8021	18.4691	37.8466
19	0.7249	0.0957	-0.2515	0.1038	-0.1194	0.174	-0.0949	-0.1176	0.0259	-0.0531	-0.0966	0.0637	-0.1208	-0.0295	-0.0917	0.086	-0.0155	-0.0157	0.0807	-0.028	0.0732	-11.8318	29.5452	37.6684

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 125:132)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 133:145)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 146:155)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 156:170)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 171:181)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 182:187)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 188:198)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 199:208)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 209:221)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 222:238)
11	X-RAY DIFFRACTION	11	chain 'A' and (resseq 239:248)
12	X-RAY DIFFRACTION	12	chain 'A' and (resseq 249:257)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 124:145)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 146:169)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 170:198)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 199:208)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 209:221)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 222:232)
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 233:257)

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