PDB-6uy1: Crystal structure of the Sth1 bromodomain from Saccharomyces cere...

ID or keywords:

Entry

Database: PDB / ID: 6uy1

Title

Crystal structure of the Sth1 bromodomain from Saccharomyces cerevisiae at 2.2 Angstrom resolution

Components

Nuclear protein STH1/NPS1

Keywords

NUCLEAR PROTEIN / STH1 /

BROMODOMAIN

Function / homology

Function and homology information

chromatin remodeling at centromere / DNA translocase activity / nucleosome disassembly / RSC-type complex / ATP-dependent chromatin remodeler activity /

chromosome, centromeric region / ATP-dependent activity, acting on DNA / cytoskeleton organization / meiotic cell cycle /

helicase activity ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.21 Å

Authors

Stavropoulos, P. / Hoelz, A.

Citation

Journal: To Be Published
Title: Crystal structure of the Sth1 bromodomain from Saccharomyces cerevisiae at 2.2 Angstrom resolution
Authors: Stavropoulos, P. / Hoelz, A.

History

Deposition	Nov 9, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 4, 2019	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6uy1.cif.gz	554.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6uy1.ent.gz	489.9 KB	Display	PDB format
PDBx/mmJSON format	6uy1.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/uy/6uy1 ftp://data.pdbj.org/pub/pdb/validation_reports/uy/6uy1	HTTPS FTP

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Related structure data

Related structure data	6mr4
Similar structure data	6mr4-3 6mr4-1 6mr4-4 6mr4-5 6kmb-2 6kmb-1 6mr4-2 4qy4-3 3aui-d 2qfd-7 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

6mr4

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Nuclear protein STH1/NPS1

B: Nuclear protein STH1/NPS1

C: Nuclear protein STH1/NPS1

D: Nuclear protein STH1/NPS1

E: Nuclear protein STH1/NPS1

F: Nuclear protein STH1/NPS1

G: Nuclear protein STH1/NPS1

H: Nuclear protein STH1/NPS1

hetero molecules

110 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Nuclear protein STH1/NPS1

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

2

B: Nuclear protein STH1/NPS1

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

3

C: Nuclear protein STH1/NPS1

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

4

D: Nuclear protein STH1/NPS1

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

5

E: Nuclear protein STH1/NPS1

hetero molecules

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

6

F: Nuclear protein STH1/NPS1

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

7

G: Nuclear protein STH1/NPS1

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

8

H: Nuclear protein STH1/NPS1

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

Unit cell

Length a, b, c (Å)	76.279, 76.281, 98.443
Angle α, β, γ (deg.)	90.000, 96.650, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Nuclear protein STH1/NPS1 / ATP-dependent helicase STH1 / Chromatin structure-remodeling complex protein STH1 / SNF2 homolog Mass: 13745.808 Da / Num. of mol.: 8 / Fragment: bromodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: STH1, NPS1, YIL126W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32597, DNA helicase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 732 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.45 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M BIS-TRIS pH 6.5 0.2 M magnesium chloride hexahydrate 25% (w/v) Polyethylene glycol 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 0.97949 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2010

Radiation

Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection

Resolution: 2.2→20 Å / Num. obs: 108351 / % possible obs: 98.9 % / Redundancy: 6.9 % / R_merge(I) obs: 0.095 / Χ²: 1.052 / Net I/σ(I): 8.8 / Num. measured all: 749157

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
2.2-2.28	3.9	0.633	10242	1.181	1	93.3
2.28-2.37	5.1	0.573	10730	1.049	1	98
2.37-2.48	6.3	0.463	10867	1.028	1	99.3
2.48-2.61	7.2	0.361	10932	1.066	1	99.5
2.61-2.77	7.7	0.272	10862	1.06	1	99.6
2.77-2.98	7.8	0.178	10921	1.041	1	99.7
2.98-3.28	7.8	0.116	10992	1.045	1	99.8
3.28-3.76	7.4	0.086	10893	1.008	1	99.6
3.76-4.72	7.9	0.071	10965	1.093	1	100
4.72-20	7.8	0.057	10947	1.017	1	99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.21→19.95 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.228	3902	3.61 %
R_work	0.184	104322	-
obs	0.1856	108224	97.53 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 247.64 Å² / B_iso mean: 65.1061 Å² / B_iso min: 27.29 Å²

Refinement step

Cycle: final / Resolution: 2.21→19.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7409	0	1	734	8144
B_iso mean	-	-	43.4	52.55	-
Num. residues	-	-	-	-	881

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.21-2.23	0.3329	85	0.3427	2232	58
2.23-2.26	0.329	141	0.3159	3584	93
2.26-2.29	0.3645	133	0.3108	3593	95
2.29-2.32	0.3007	139	0.2717	3653	96
2.32-2.35	0.2466	141	0.2525	3733	98
2.35-2.39	0.3114	147	0.2461	3867	99
2.39-2.43	0.3038	136	0.2395	3663	99
2.43-2.47	0.3176	141	0.2362	3879	99
2.47-2.51	0.2956	141	0.2225	3768	99
2.51-2.55	0.3011	143	0.2141	3793	100
2.55-2.6	0.2212	145	0.2094	3795	99
2.6-2.66	0.3003	140	0.2099	3790	100
2.66-2.71	0.3075	145	0.208	3841	100
2.71-2.78	0.2942	141	0.211	3773	100
2.78-2.85	0.2391	142	0.2013	3821	100
2.85-2.92	0.2816	143	0.2008	3809	100
2.92-3.01	0.23	138	0.1993	3769	100
3.01-3.11	0.2792	145	0.209	3843	100
3.11-3.22	0.2601	142	0.204	3800	100
3.22-3.34	0.2085	139	0.1888	3821	100
3.34-3.5	0.2423	142	0.1847	3821	100
3.5-3.68	0.2101	143	0.172	3769	99
3.68-3.91	0.2067	141	0.1547	3807	100
3.91-4.21	0.1583	143	0.1406	3822	100
4.21-4.63	0.1825	144	0.1376	3813	100
4.63-5.28	0.1718	144	0.1474	3818	100
5.28-6.62	0.2331	139	0.165	3837	100
6.62-19.95	0.1952	139	0.1715	3808	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	7.8118	-4.4238	6.0033	8.7154	-7.165	7.1896	0.2289	-0.2298	-0.6035	0.3348	0.6107	1.1793	-0.1532	-1.3582	-0.8107	0.4696	0.0618	0.0906	0.6536	0.0458	0.5423	59.0347	33.2486	128.8935
2	5.8025	0.0709	-1.9018	0.6665	0.4166	3.2565	0.0742	-0.3282	0.0115	-0.0288	-0.1021	-0.1717	-0.1775	0.0497	0.0977	0.38	0.0462	0.0322	0.2858	-0.0061	0.3221	74.0671	35.3586	120.8827
3	4.0078	1.7223	-1.4464	6.2747	-1.5567	5.2141	0.427	-0.474	0.1299	0.9397	-0.188	-0.0972	-0.506	0.2261	-0.2509	0.424	0.0288	0.0053	0.412	-0.0462	0.344	73.3937	36.7886	130.6178
4	3.9962	1.4092	-1.7116	4.2689	-0.0721	4.5137	0.3131	-0.4772	0.3204	0.8372	-0.1628	0.4514	-0.9974	-0.3921	-0.4745	0.4704	0.1088	0.1346	0.3981	-0.0318	0.4529	66.2208	44.6596	129.5449
5	5.1544	4.1413	-4.5445	7.2768	-4.4425	7.704	-0.1212	-0.7084	0.421	-0.2666	0.6448	1.6847	-0.3028	-2.429	-0.3837	0.4725	0.1377	-0.0581	0.7196	-0.0521	0.6375	56.1491	42.0414	103.8451
6	3.6541	0.0185	-0.4121	3.3467	-1.8375	4.6488	-0.0702	0.1952	-0.1828	-0.1503	0.126	-0.0614	-0.0269	-0.0264	-0.0207	0.4399	0.0411	-0.0075	0.3524	-0.0187	0.4048	73.7028	37.8934	109.2965
7	8.4279	-1.7347	3.0251	3.9455	-0.5837	6.2378	0.2321	0.3936	-0.2596	-0.441	-0.1306	0.2528	0.248	-0.1773	-0.1349	0.3853	0.0007	-0.0029	0.3234	-0.0348	0.3311	66.2837	36.0203	100.1381
8	8.1091	0.3109	1.2974	4.2643	-0.65	2.909	-0.023	0.3157	-0.0493	-0.1768	-0.0895	-0.4279	0.0282	0.2847	0.1473	0.3659	0.008	0.0104	0.4169	-0.1041	0.3147	70.2916	44.5069	62.3707
9	9.0399	0.194	-2.8702	5.5142	0.0364	6.0397	0.0601	0.3882	0.5249	-0.2931	-0.0245	-0.549	-0.4684	0.4024	-0.0177	0.3651	-0.0081	-0.0309	0.418	-0.0073	0.3437	72.856	52.3519	60.5819
10	3.7771	-0.259	-5.2559	5.5587	2.6518	8.5462	-0.1467	-0.3145	0.1182	0.5216	-0.3221	-1.1566	0.4627	1.9978	0.5093	0.5079	0.1299	-0.0871	0.5909	0.0315	0.623	77.0924	30.0492	80.042
11	8.2213	-0.6077	0.1453	2.9633	-1.8091	2.0094	-0.0375	0.3529	-0.2889	-0.0784	-0.0032	-0.0389	0.2232	-0.1681	0.0776	0.4437	0.0209	-0.0254	0.4043	-0.1186	0.2765	62.2509	36.7233	70.0251
12	5.3092	-0.6609	4.4698	2.7147	-1.9853	6.1089	0.1357	-0.0058	-0.3978	0.0945	-0.0168	0.1096	0.7852	-0.2335	-0.0549	0.4323	0.0444	0.0375	0.3575	-0.0414	0.4153	63.7365	28.4808	77.2693
13	6.3521	-1.4962	-0.1759	7.6709	0.7261	2.9397	-0.08	0.1188	-0.832	-0.4144	-0.0226	-0.732	1.4025	0.2686	0.1267	0.5105	0.1769	0.073	0.4054	-0.1255	0.5367	70.8879	22.7291	70.3997
14	7.6473	3.2456	3.6835	5.651	2.3426	6.7237	-0.1591	1.5534	-0.1891	-0.162	0.4146	2.3366	0.8319	-1.4328	-0.0401	0.6125	-0.1591	-0.1057	1.1297	-0.1048	1.3889	17.4585	33.3606	62.0362
15	1.897	0.6633	0.437	6.8767	-4.2634	3.2215	-0.1512	-0.7505	0.7332	1.4441	0.8748	1.2481	-1.053	-0.5694	-0.5805	0.6023	0.0738	0.1134	0.6353	-0.0435	0.8844	24.8222	48.6431	68.594
16	6.7327	0.1476	-0.4248	2.6633	-0.7477	1.8577	0.1055	0.7035	-1.1991	-0.6094	0.0114	0.5763	0.504	0.2536	-0.1175	0.5431	0.0666	-0.1401	0.5894	-0.2458	0.7363	36.9938	33.9939	61.3914
17	6.9153	-3.2443	1.8117	9.7782	2.2824	2.3393	-0.3829	0.7328	-1.5967	-0.8129	1.9502	1.5451	0.8973	0.9248	-1.4314	0.6822	-0.0089	-0.2095	0.7917	-0.3058	1.6795	23.4018	21.8508	60.9063
18	3.6062	0.9368	0.6279	3.7496	-0.3889	5.5688	0.3152	-0.5769	-0.7343	0.4101	-0.1257	1.2147	0.3859	-0.907	-0.1391	0.4318	-0.0011	0.0652	0.7377	0.0428	0.9264	28.3836	35.6749	72.8573
19	8.1495	4.6948	0.1803	3.6191	-2.622	8.2279	-0.4141	1.0373	0.9926	-0.0498	0.0156	-1.2096	-0.4334	2.5807	0.1119	0.4226	-0.139	-0.1112	1.0937	0.1015	1.0739	43.5766	41.7536	120.5572
20	4.6809	-3.1971	4.9858	5.4957	-3.1123	5.9898	0.0136	1.2053	-1.8518	-0.2288	-0.3093	0.2813	1.3292	1.3393	0.0143	0.5575	0.1165	0.1216	0.7121	-0.1395	0.7048	37.0934	28.3075	112.2657
21	8.4165	0.2698	2.4744	3.9188	0.2348	5.0063	-0.0913	-0.4113	0.5633	0.3362	-0.0884	-0.5172	-0.3351	0.4723	0.2326	0.4662	-0.0515	0.0167	0.3967	-0.0345	0.5271	25.4009	43.7461	119.0178
22	7.6855	0.6901	1.2594	4.143	0.0074	4.7635	0.0061	-0.6179	-0.1912	0.7592	0.1146	-0.8875	0.2853	0.5649	-0.1234	0.3615	0.0418	-0.065	0.5052	-0.0751	0.5407	33.3934	34.9812	125.8883
23	3.1009	3.1451	1.6966	3.6711	3.4832	7.5739	0.3513	0.3104	-0.2337	-0.9515	-0.4962	1.8885	-0.1941	-1.0507	-0.0263	0.5735	0.1533	-0.2424	0.8076	-0.0383	0.8469	22.1852	59.8425	56.9549
24	2.1401	-1.4278	-1.0098	3.5897	-1.0637	1.5691	0.2673	0.6557	-0.5634	-0.4073	-0.3037	0.7839	0.146	-0.174	0.0831	0.4165	0.0639	-0.1162	0.5007	-0.1987	0.4733	36.435	47.0554	60.1216
25	3.5094	-1.5896	0.7593	3.8852	0.1428	1.689	0.3964	1.29	-0.0078	-1.0658	-0.3901	0.1316	-0.2516	0.3437	0.0147	0.6341	0.0926	-0.1529	0.8473	0.0337	0.4657	34.3933	57.2663	53.358
26	7.9982	2.2232	-2.5294	8.7763	0.4689	8.22	0.1013	0.9319	-0.2875	-0.5703	0.2178	-1.4492	0.2	1.8174	-0.2388	0.5834	0.1314	0.1362	1.2572	-0.0274	0.7702	40.4476	31.0963	97.5799
27	6.9146	1.8616	0.9732	2.5726	1.4444	3.8375	0.1607	0.2789	0.1051	0.0055	-0.0321	-0.28	-0.1323	0.6858	-0.1071	0.4227	-0.0154	0.0756	0.4986	-0.0473	0.4979	26.153	36.7222	107.5446
28	6.2936	-2.524	-2.2158	4.8393	1.2257	4.5078	0.1379	1.2343	-0.4513	-0.765	-0.2001	0.1029	0.0565	0.0884	-0.0899	0.5824	0.0039	0.1018	0.9025	-0.0893	0.4957	26.5083	32.6914	95.8278
29	6.1962	-2.8568	-6.4712	3.7794	1.9528	7.1158	0.1087	1.0627	0.5939	-1.4285	-0.1072	-0.5343	-1.2456	0.6328	-0.565	0.6324	-0.1956	0.2536	1.0471	0.052	0.6077	34.2701	42.1099	94.6166

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 34 )	A	19 - 34
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 35 through 76 )	A	35 - 76
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 77 through 107 )	A	77 - 107
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 108 through 128 )	A	108 - 128
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 19 through 34 )	B	19 - 34
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 35 through 69 )	B	35 - 69
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 70 through 129 )	B	70 - 129
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 20 through 69 )	C	20 - 69
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 70 through 129 )	C	70 - 129
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 19 through 34 )	D	19 - 34
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 35 through 69 )	D	35 - 69
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 70 through 107 )	D	70 - 107
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 108 through 129 )	D	108 - 129
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 19 through 34 )	E	19 - 34
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 35 through 45 )	E	35 - 45
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 46 through 77 )	E	46 - 77
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 78 through 85 )	E	78 - 85
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 86 through 127 )	E	86 - 127
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 20 through 34 )	F	20 - 34
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 35 through 45 )	F	35 - 45
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 46 through 78 )	F	46 - 78
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 79 through 128 )	F	79 - 128
23	X-RAY DIFFRACTION	23	chain 'G' and (resid 19 through 34 )	G	19 - 34
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 35 through 63 )	G	35 - 63
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 64 through 129 )	G	64 - 129
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 20 through 34 )	H	20 - 34
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 35 through 63 )	H	35 - 63
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 64 through 107 )	H	64 - 107
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 108 through 129 )	H	108 - 129

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