PDB-6kmb: Crystal structure of Sth1 bromodomain

ID or keywords:

Entry

Database: PDB / ID: 6kmb

Title

Crystal structure of Sth1 bromodomain

Components

Nuclear protein STH1/NPS1

Keywords

GENE REGULATION / Chromatin remodeling / histone acetylation / RSC complex / Sth1 / bromodomain

Function / homology

Function and homology information

: / DNA translocase activity / nucleosome array spacer activity / RSC-type complex / ATP-dependent chromatin remodeler activity / nucleosome disassembly / histone H4 reader activity / chromosome, centromeric region / : / cytoskeleton organization ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Chen, G. / Li, W. / Yan, F. / Wang, D. / Chen, Y.

Funding support

China, 1items

Citation

Journal: Structure / Year: 2020
Title: The Structural Basis for Specific Recognition of H3K14 Acetylation by Sth1 in the RSC Chromatin Remodeling Complex.
Authors: Chen, G. / Li, W. / Yan, F. / Wang, D. / Chen, Y.

History

Deposition	Jul 31, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 30, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 27, 2019	Group: Database references / Category: citation Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 22, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3	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	6kmb.cif.gz	197.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6kmb.ent.gz	159.5 KB	Display	PDB format
PDBx/mmJSON format	6kmb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6kmb_validation.pdf.gz	460.3 KB	Display	wwPDB validaton report
Full document	6kmb_full_validation.pdf.gz	465.2 KB	Display
Data in XML	6kmb_validation.xml.gz	18.4 KB	Display
Data in CIF	6kmb_validation.cif.gz	24.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/km/6kmb ftp://data.pdbj.org/pub/pdb/validation_reports/km/6kmb	HTTPS FTP

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Related structure data

Related structure data	6kmjC 2grcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6mr4-5 6mr4-1 6mr4-3 6uy1-8 6uy1-6 6uy1-1 2bl8-3 3ms6-d 6mr4-6 6mr4-4 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

6kmjC

2grcS

S: Starting model for refinement

C: citing same article (ref.)

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

hetero molecules

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

1

A: Nuclear protein STH1/NPS1

defined by author
Evidence: light scattering, The protein is monomer in solution determined by size exclusion chromatography coupled with multi-angle light scattering (SEC-MALS) analysis.
13.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Nuclear protein STH1/NPS1

hetero molecules

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

3

C: Nuclear protein STH1/NPS1

hetero molecules

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

4

D: Nuclear protein STH1/NPS1

hetero molecules

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

Unit cell

Length a, b, c (Å)	108.855, 108.855, 110.928
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Nuclear protein STH1/NPS1 / ATP-dependent helicase STH1 / Chromatin structure-remodeling complex protein STH1 / SNF2 homolog Mass: 13334.953 Da / Num. of mol.: 4 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) / Variant (production host): Rosetta / References: UniProt: P32597, DNA helicase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.56 Å³/Da / Density % sol: 65.42 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M sodium formate, pH 7.0, 20% w/v PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.9785 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.9785 Å / Relative weight: 1

Reflection

Resolution: 2.4→50 Å / Num. obs: 29241 / % possible obs: 100 % / Redundancy: 10.3 % / B_iso Wilson estimate: 33.33 Å² / R_merge(I) obs: 0.08 / R_pim(I) all: 0.026 / R_rim(I) all: 0.084 / Χ²: 0.983 / Net I/σ(I): 7.9 / Num. measured all: 299963

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.4-2.44	10.2	0.713	1442	0.89	0.234	0.751	0.917	100
2.44-2.49	10.4	0.582	1471	0.91	0.189	0.613	0.93	100
2.49-2.53	10.5	0.551	1454	0.92	0.178	0.579	0.941	100
2.53-2.59	10.4	0.489	1452	0.941	0.159	0.514	0.945	100
2.59-2.64	10.3	0.427	1449	0.958	0.14	0.449	0.957	100
2.64-2.7	10.1	0.372	1457	0.957	0.123	0.392	1.041	100
2.7-2.77	9.7	0.309	1476	0.973	0.104	0.326	0.991	100
2.77-2.85	9.5	0.258	1443	0.977	0.088	0.273	1.039	100
2.85-2.93	10.6	0.212	1457	0.985	0.068	0.223	1.052	100
2.93-3.02	10.6	0.189	1466	0.988	0.061	0.199	1.022	100
3.02-3.13	10.6	0.146	1454	0.993	0.047	0.154	1.07	100
3.13-3.26	10.6	0.129	1446	0.994	0.041	0.135	1.122	99.9
3.26-3.41	10.4	0.1	1467	0.996	0.032	0.105	1.118	100
3.41-3.58	10	0.086	1455	0.997	0.029	0.091	1.178	100
3.58-3.81	9.7	0.068	1456	0.998	0.023	0.072	1.166	100
3.81-4.1	10.8	0.059	1468	0.998	0.019	0.062	1.118	100
4.1-4.52	10.6	0.053	1465	0.998	0.017	0.055	0.996	100
4.52-5.17	10.2	0.05	1479	0.998	0.016	0.052	0.862	100
5.17-6.51	10	0.045	1474	0.999	0.015	0.047	0.682	100
6.51-35.6	10	0.034	1510	0.999	0.011	0.036	0.507	99.9

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2GRC

2grc

Resolution: 2.4→35.631 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.31

	R_factor	Num. reflection	% reflection
R_free	0.2423	1471	5.07 %
R_work	0.1983	-	-
obs	0.2006	29037	99.45 %

Solvent computation

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

Displacement parameters

B_iso max: 120.31 Å² / B_iso mean: 46.0154 Å² / B_iso min: 15.78 Å²

Refinement step

Cycle: final / Resolution: 2.4→35.631 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3652	0	18	81	3751
B_iso mean	-	-	61.25	34.62	-
Num. residues	-	-	-	-	435

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3762
X-RAY DIFFRACTION	f_angle_d	0.61	5076
X-RAY DIFFRACTION	f_chiral_restr	0.042	532
X-RAY DIFFRACTION	f_plane_restr	0.004	658
X-RAY DIFFRACTION	f_dihedral_angle_d	21.426	2274

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 (%)
2.4003-2.4778	0.3162	113	0.2601	2396	95
2.4778-2.5663	0.3015	127	0.252	2517	100
2.5663-2.669	0.3082	135	0.2464	2511	100
2.669-2.7904	0.2912	134	0.2421	2503	100
2.7904-2.9375	0.298	126	0.234	2532	100
2.9375-3.1214	0.2919	143	0.2502	2496	100
3.1214-3.3623	0.2666	147	0.2176	2506	100
3.3623-3.7003	0.2736	139	0.1932	2522	100
3.7003-4.235	0.1897	137	0.1679	2499	100
4.235-5.3328	0.1952	146	0.1569	2527	100
5.3328-35.6	0.1911	124	0.1641	2557	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	7.9544	-3.7634	1.4967	6.3209	-2.0312	3.9589	0.1357	0.504	-0.0993	-0.6954	-0.1565	-0.7797	0.3466	0.5938	0.0868	0.3599	0.0523	0.1327	0.3444	-0.0629	0.3345	67.3929	69.9553	-4.6568
2	6.7463	2.2705	-3.7455	3.1827	-2.5981	7.7508	0.1534	-0.511	-0.3182	0.1564	-0.2758	0.0483	-0.2832	0.1603	0.0736	0.2075	-0.0405	-0.0473	0.2119	0.0237	0.2421	57.9197	66.7719	12.786
3	4.3445	1.3902	2.0423	2.785	-0.5157	5.2477	-0.1029	-0.0693	0.159	-0.0442	0.1981	-0.2063	-0.068	-0.1377	-0.0593	0.1595	0.046	-0.006	0.1937	0.0071	0.2145	58.395	76.6904	3.7861
4	5.276	-0.8136	1.5006	7.2948	-3.9561	5.8974	-0.2987	0.0123	0.2918	-0.3131	0.0185	-0.9582	0.0162	0.1192	0.4094	0.1757	-0.001	0.063	0.2929	-0.0546	0.342	71.2312	75.6485	3.7666
5	5.3539	3.0867	2.0245	3.7199	1.5847	2.8354	-0.0757	-0.6656	-0.2261	0.455	-0.1253	0.6332	0.3999	-0.248	0.1232	0.4001	-0.0282	0.0763	0.4688	0.0998	0.2805	52.29	66.5127	50.2647
6	7.0644	1.38	-5.1015	2.8457	-0.6001	3.8245	-0.0906	0.4961	-0.7911	-0.1123	-0.3711	-0.1842	0.0156	-0.3212	0.3703	0.1774	0.0239	-0.0418	0.3669	0.0278	0.2731	63.0835	65.0909	32.4028
7	5.2445	0.913	3.1882	3.0668	1.3526	3.6356	0.0048	-0.1304	0.2835	-0.2258	0.0155	0.092	-0.1931	0.1616	-0.0771	0.2264	-0.0281	0.0098	0.26	0.015	0.2254	58.1631	76.1242	40.7396
8	4.9645	-0.5733	0.0586	7.745	1.393	4.2998	0.0047	-0.41	-0.1189	-0.0696	0.1207	0.9002	-0.1218	-0.6927	0.0899	0.229	-0.0411	0.0206	0.3767	0.0927	0.3519	46.3733	70.0205	41.5889
9	5.522	0.5863	0.7849	2.5197	2.2303	4.9814	0.1943	1.0531	-0.5979	-1.0025	-0.1274	-1.4349	0.0382	0.4937	0.1276	0.9016	0.1081	0.3246	0.5261	-0.0309	0.7999	76.4827	50.5733	-5.6089
10	3.9903	-5.5677	0.1705	8.1373	-0.7544	2.2624	0.4515	0.1534	-0.8566	-1.2017	-0.0648	0.2701	-0.0436	-0.2994	-0.1658	0.7252	0.0368	-0.0509	0.3524	-0.0344	0.4928	60.2948	58.2971	-4.3611
11	0.8132	-0.4481	0.7636	4.1129	2.3956	2.7034	-0.1126	-0.257	-0.3846	-0.1498	-0.3999	-0.3079	0.2896	-0.5158	0.4159	0.2769	0.0546	0.0291	0.3948	0.0497	0.4588	68.9578	57.4673	15.432
12	4.1518	1.2817	-0.3382	4.3816	1.0707	3.4974	-0.1918	0.135	-0.839	-0.6851	0.09	-0.4379	0.5975	0.3645	0.091	0.5936	0.1122	0.0941	0.283	-0.0523	0.5366	68.2218	47.0486	4.0418
13	4.9989	3.4164	-2.1962	6.0634	-2.9156	1.5504	0.386	-1.392	-0.3915	1.3126	-0.1748	0.3311	0.3211	-0.4943	-0.2077	0.6469	-0.0498	0.056	0.5965	0.166	0.3803	52.3439	46.8381	51.1827
14	4.1246	3.6796	-5.8746	8.1536	-4.696	8.4668	0.5152	-0.4339	-0.0968	0.4993	-0.4011	-0.7432	0.0613	1.1599	-0.2886	0.4411	-0.0145	-0.096	0.4856	0.0169	0.3731	64.0219	59.1004	49.1661
15	1.6736	0.2838	1.0961	2.6507	-0.6079	6.4654	-0.0678	-0.1131	-0.0074	-0.1348	-0.157	-0.0568	-0.0519	0.4593	0.177	0.2475	-0.0223	-0.0151	0.2557	0.0879	0.3	55.9266	54.5569	30.2096
16	2.3537	-0.2742	1.5955	4.7191	-1.4073	3.7759	-0.1264	-0.5482	-1.0326	0.1318	-0.1258	0.644	0.8128	-0.4276	0.2761	0.5497	-0.0715	0.0221	0.3237	0.1492	0.5163	50.6923	42.81	38.4815
17	7.7814	3.4555	-5.2785	6.3404	-2.1383	5.0602	-0.3201	0.0557	-0.3621	-0.2682	0.3816	-0.1861	1.1324	-0.093	0.014	0.4996	-0.0557	-0.02	0.3548	0.1493	0.5343	61.4052	43.3112	38.3498
18	3.8011	1.0915	3.6682	1.6918	1.6622	3.8022	-0.1893	-0.6252	-0.4622	-0.5495	0.1012	-0.7414	-0.0471	0.6861	0.0235	0.3718	0.006	-0.0338	0.421	0.0399	0.487	71.6499	55.6405	34.8538
19	4.1849	-0.2866	-0.1987	5.9354	-4.098	5.5334	-0.0296	-0.7866	-0.5505	1.1314	0.0791	-0.383	0.3434	0.2191	0.0567	0.6037	0.0575	-0.1449	0.4749	0.1138	0.4615	64.9259	46.3519	47.5613

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1249 through 1275 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1276 through 1299 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1300 through 1332 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1333 through 1358 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1249 through 1275 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1276 through 1293 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1294 through 1332 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1333 through 1357 )	B
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1250 through 1263 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1264 through 1275 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1276 through 1293 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1294 through 1357 )	C
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 1251 through 1264 )	D
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 1265 through 1275 )	D
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 1276 through 1293 )	D
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1294 through 1314 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1315 through 1332 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 1333 through 1337 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1338 through 1358 )	D

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi