PDB-4xs5: Crystal structure of Sulfate transporter/antisigma-factor antagon...

ID or keywords:

Entry

Database: PDB / ID: 4xs5

Title

Crystal structure of Sulfate transporter/antisigma-factor antagonist STAS from Dyadobacter fermentans DSM 18053

Components

Sulfate transporter/antisigma-factor antagonist STAS

Keywords

TRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG

Function / homology

STAS domain / Transcription Regulator spoIIAA / STAS domain / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta / Sulfate transporter/antisigma-factor antagonist STAS

Function and homology information

Biological species

Dyadobacter fermentans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.9 Å

Authors

Chang, C. / Cuff, M. / Chhor, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To Be Published
Title: Crystal structure of Sulfate transporter/antisigma-factor antagonist STAS from Dyadobacter fermentans DSM 18053
Authors: Chang, C. / Cuff, M. / Chhor, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Jan 21, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 11, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Derived calculations / Refinement description / Source and taxonomy Category: entity_src_gen / pdbx_struct_oper_list / software Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	4xs5_validation.pdf.gz	450.8 KB	Display	wwPDB validaton report
Full document	4xs5_full_validation.pdf.gz	453.6 KB	Display
Data in XML	4xs5_validation.xml.gz	18.1 KB	Display
Data in CIF	4xs5_validation.cif.gz	24.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xs/4xs5 ftp://data.pdbj.org/pub/pdb/validation_reports/xs/4xs5	HTTPS FTP

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Related structure data

Similar structure data	4n36-4 4n32-3 4n37-2 5eel-3 4n37-4 4n32-4 5eel-2 4n38-4 2ppp-d 2py2-4 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 - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC103436

Similar structure data

Other databases

TargetTrack: MCSG-APC103436

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (3)

Deposited unit

A: Sulfate transporter/antisigma-factor antagonist STAS

B: Sulfate transporter/antisigma-factor antagonist STAS

C: Sulfate transporter/antisigma-factor antagonist STAS

D: Sulfate transporter/antisigma-factor antagonist STAS

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

1

A: Sulfate transporter/antisigma-factor antagonist STAS

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

2

B: Sulfate transporter/antisigma-factor antagonist STAS

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

3

C: Sulfate transporter/antisigma-factor antagonist STAS

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

4

D: Sulfate transporter/antisigma-factor antagonist STAS

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

Unit cell

Length a, b, c (Å)	83.111, 84.520, 109.681
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

biological unit is the same as asym.

#1: Protein	Sulfate transporter/antisigma-factor antagonist STAS Mass: 16213.268 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / NS114) (bacteria) Strain: ATCC 700827 / DSM 18053 / NS114 / Gene: Dfer_5480 / Plasmid: pMCSG57 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: C6VVE1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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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 Å³/Da / Density % sol: 59.07 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.0 M Ammonium Sulfate, 0.1 M Tris pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2012
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97931 Å / Relative weight: 1
Reflection	Resolution: 2.9→50 Å / Num. all: 17843 / Num. obs: 17637 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / R_merge(I) obs: 0.052 / Net I/σ(I): 27.12
Reflection shell	Resolution: 2.9→2.95 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.739 / Mean I/σ(I) obs: 2.18 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.15	data extraction
SBC-Collect		data collection
HKL-3000		phasing
Coot		model building
HKL-3000		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 2.9→40.25 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.89 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2599	1593	5.05 %	random
R_work	0.2071	-	-	-
obs	0.2096	17494	94.59 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.9→40.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3684	0	0	51	3735

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3754
X-RAY DIFFRACTION	f_angle_d	0.63	5093
X-RAY DIFFRACTION	f_dihedral_angle_d	10.53	1363
X-RAY DIFFRACTION	f_chiral_restr	0.025	606
X-RAY DIFFRACTION	f_plane_restr	0.002	656

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 (%)
2.8913-2.9846	0.3598	129	0.3114	1986	X-RAY DIFFRACTION	70
2.9846-3.0913	0.3498	134	0.2868	2562	X-RAY DIFFRACTION	89
3.0913-3.215	0.3167	154	0.275	2852	X-RAY DIFFRACTION	98
3.215-3.3612	0.3463	167	0.2542	2823	X-RAY DIFFRACTION	99
3.3612-3.5383	0.2938	128	0.2261	2845	X-RAY DIFFRACTION	99
3.5383-3.7599	0.2077	146	0.1995	2851	X-RAY DIFFRACTION	99
3.7599-4.0499	0.2596	155	0.1763	2823	X-RAY DIFFRACTION	98
4.0499-4.457	0.2014	147	0.1585	2817	X-RAY DIFFRACTION	98
4.457-5.1009	0.2308	195	0.1548	2760	X-RAY DIFFRACTION	98
5.1009-6.4223	0.2346	121	0.2113	2845	X-RAY DIFFRACTION	98
6.4223-40.2539	0.2454	117	0.2075	2792	X-RAY DIFFRACTION	96

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	1.9717	-0.9873	-1.4795	5.0176	-0.922	2.3434	-0.1266	0.2171	-0.0102	-0.1084	0.1678	-0.0635	-0.1486	0.2524	0.0255	0.395	-0.3564	-0.128	0.5946	-0.0159	0.1659	18.7086	-1.7451	20.1475
2	1.4719	0.4304	0.7791	1.737	0.7747	1.5116	-0.0797	0.4744	-0.3575	-0.383	0.1651	0.1039	0.078	0.2389	-0.2796	0.2953	-0.2902	-0.0551	0.6285	-0.2788	0.2685	15.3658	-10.2951	16.9863
3	1.3462	2.3144	1.0635	4.369	2.2617	1.7192	-0.0879	0.0778	-0.2707	-0.021	-0.0075	0.0568	0.0522	-0.164	-0.1028	0.3354	-0.1211	-0.2233	0.5846	-0.1129	0.7174	2.2605	-7.7903	18.1455
4	2.5356	0.8717	1.1326	2.6199	0.5678	3.7373	-0.0845	0.1609	-0.3539	0.2011	0.0152	0.0422	0.6571	0.1076	-0.105	0.3456	-0.0324	-0.0848	0.2576	-0.1346	0.4173	12.0204	-13.5523	24.9385
5	5.1841	2.2358	-1.9234	4.2594	2.6029	7.7168	-0.0401	-0.2075	-0.0549	0.2506	0.1265	0.4411	-0.1041	-0.354	-0.0528	0.8538	-0.3324	0.3948	1.1901	-0.2215	0.8856	-0.9214	-10.7871	26.7194
6	1.1226	1.4077	-1.8996	7.8347	-3.7787	3.7971	0.0369	-0.6475	-0.2602	0.8471	-0.0494	-0.6435	0.0745	0.4394	-0.0111	0.9756	-0.1675	-0.0654	0.6418	-0.1462	0.9095	8.6219	-16.1783	30.7887
7	5.3392	-0.1774	3.3539	1.4793	-0.5738	4.0395	-0.3286	-0.4794	-0.0901	0.5528	0.0072	0.0305	0.2265	-0.3288	0.132	0.3047	0.048	0.0206	0.2227	0.016	0.1545	15.8648	-4.389	35.0983
8	4.0398	-1.1459	0.7864	6.1183	-0.8725	3.7753	-0.0967	-0.374	0.2239	0.4423	0.015	-0.1766	-0.3529	0.045	0.0538	0.6843	0.0201	-0.3062	0.4242	-0.0499	0.8127	23.5252	18.6569	46.9398
9	6.0373	-1.3923	-0.9337	1.6347	-0.3426	0.8486	-0.2249	-0.1367	0.3529	-0.1125	0.0159	-0.1648	-0.3714	-0.0195	0.0843	0.8042	0.066	-0.086	0.4428	0.1319	1.1559	17.2294	28.7535	40.2565
10	3.9163	1.2605	1.0945	4.2508	-0.3005	1.1796	0.1244	-0.1349	0.2559	0.1361	-0.0943	-0.3927	-0.3932	0.4722	-0.0284	0.4215	0.0737	-0.1242	0.417	0.0239	0.7778	24.4421	19.8758	40.5325
11	2.4823	-2.3042	0.9122	2.2326	-1.3548	4.3613	-0.0066	0.0515	0.1958	0.0112	-0.0234	-0.0607	-0.1078	-0.089	0.0356	0.9115	0.5263	0.2289	0.7672	0.0711	0.8827	6.4253	24.7426	43.2154
12	3.8934	-1.0746	2.4186	3.444	-1.5823	2.03	0.4395	0.4855	0.2971	-0.325	-0.2098	-0.1704	-0.1264	0.06	-0.0136	0.5607	0.3321	0.0822	0.7654	0.3177	0.7464	16.0191	22.9551	31.267
13	4.6736	-2.9237	-1.3429	4.8647	-0.09	3.2154	0.1501	0.0065	-0.0333	0.0596	0.0048	0.0579	-0.2411	-0.1936	-0.0495	0.3758	0.2379	0.0884	0.2721	0.1822	0.3991	14.5424	14.9009	40.047
14	5.6653	2.9969	-0.0221	5.6907	0.9617	0.5292	0.0323	-0.0017	-0.2556	-0.0943	0.0086	0.4885	0.1631	-0.5523	-0.0586	0.6334	0.2244	-0.2272	0.7065	0.1579	1.1854	1.4079	17.5983	37.6382
15	6.6456	-2.8425	2.452	6.5104	-2.8781	5.6166	-0.1052	0.4799	0.299	-0.471	-0.0156	0.069	-0.1954	0.0878	0.1482	0.5229	0.0844	0.0505	0.3991	0.1981	0.322	9.4356	14.3064	37.8857
16	3.8088	-0.6711	1.7512	6.9893	1.7734	3.4977	-0.1316	0.1339	-0.2547	-0.1899	-0.0544	-0.1177	-0.0279	-0.0257	0.006	0.2911	0.1146	-0.0084	0.1661	0.0058	0.2198	20.3924	6.4643	40.1082
17	2.2808	1.0043	-0.8397	2.7951	0.6721	4.1255	0.2863	-0.3752	0.2549	0.2863	-0.0808	0.0988	-0.1661	-0.0166	0.0408	0.8998	-0.3677	0.2134	0.6211	-0.0225	0.3035	21.3976	5.5217	17.4659
18	1.925	-0.1534	0.9639	3.5459	2.2487	3.0334	0.2705	-0.2913	0.0505	0.3588	-0.1278	-0.2119	0.3378	0.4174	-0.2327	0.6723	-0.2812	-0.0486	0.3905	-0.0626	0.1824	26.7048	6.1584	12.7409
19	3.6717	-0.0001	0.2308	2.0941	0.1185	1.7596	0.353	-0.4839	0.5706	0.1406	-0.1186	-0.1599	0.2871	0.2733	-0.1853	0.572	-0.114	0.1329	0.3087	-0.0598	0.2323	24.7303	10.346	9.5338
20	2.4551	0.3616	0.4438	6.2431	3.4136	4.6746	0.4174	0.3088	0.1319	-0.1293	-0.2687	-0.4191	0.396	0.3946	-0.0536	0.349	0.0225	-0.0838	0.3636	-0.0382	0.3241	34.5657	9.8013	5.4794
21	6.3276	0.541	-0.8451	5.4598	0.3669	2.0065	0.2316	-0.1305	0.5927	0.221	-0.1761	0.62	-0.1615	-0.2174	-0.1237	0.2109	-0.0914	0.1657	0.2152	-0.0201	0.4555	20.3478	15.5092	5.0752
22	3.4219	0.9309	-0.9021	2.839	0.4784	2.8063	-0.005	0.3505	0.6939	-0.2472	-0.1695	0.103	-0.5956	0.0891	0.0682	0.3749	-0.1609	0.0115	0.4863	-0.0485	0.4536	27.505	23.2327	3.7231
23	1.1356	0.2264	0.1175	2.8705	1.1646	2.3276	0.2319	0.201	0.1092	-0.2638	-0.0232	-0.0265	-0.2488	0.1178	-0.0487	0.2618	0.0424	0.0193	0.2526	0.0581	0.0651	23.1112	5.9282	-5.5314
24	0.9965	-1.5098	0.6148	2.7923	-0.3878	0.9669	-0.0614	-0.0888	-0.3203	-0.295	-0.0134	-0.1002	0.2609	0.1163	0.1668	0.8012	0.1832	0.3505	0.7212	0.5291	1.1361	42.4832	1.4401	30.7157
25	4.6104	0.7763	1.7196	2.4036	-1.8427	2.9587	-0.0409	-0.0724	0.1577	0.0397	-0.0119	0.2299	-0.2227	-0.1384	0.0453	0.6164	0.3971	0.239	0.7753	0.3944	1.0306	36.2838	1.8259	35.063
26	5.744	-2.512	-1.8661	6.6507	2.203	1.0572	0.0484	0.4901	0.3377	-0.4518	-0.2817	0.102	-0.1446	0.16	0.2083	0.6421	0.303	0.3019	0.678	0.4105	0.9165	50.8986	-9.7482	33.9335
27	1.3762	-0.3769	0.9723	2.3387	-0.5331	0.8755	0.0791	-0.3058	0.6736	-0.0227	-0.0061	-0.1481	-0.1511	0.0803	-0.154	0.4245	0.036	0.189	0.6643	0.4562	1.449	50.0125	2.706	39.9605
28	2.9565	2.3443	0.786	6.0669	-1.2205	1.8167	0.0031	-0.0026	0.6202	0.088	0.0257	-0.0949	-0.481	-0.0027	-0.0773	0.4771	0.1728	0.1087	0.3062	0.1694	0.8929	39.7106	2.9399	39.5752
29	2.5483	-2.1597	1.7463	2.0965	-1.1805	2.4583	-0.0523	0.0373	0.1566	0.0359	0.0754	0.0239	-0.11	-0.1342	0.067	0.5193	0.2933	0.235	0.6092	0.3629	0.7764	47.5665	-13.4116	37.0602
30	2.9817	-0.7735	-0.2783	2.2022	0.0324	2.4152	-0.1424	-0.4981	0.5526	0.154	0.2122	-0.1137	-0.2703	-0.2403	-0.1913	0.2883	0.1102	-0.0824	0.6319	-0.2512	1.0747	45.0908	-1.76	48.2935
31	5.9236	0.096	-0.6781	3.2963	4.7614	8.5173	0.0649	0.4112	-0.4563	-0.4114	-0.1976	0.2082	0.4984	0.0476	0.1332	0.4211	0.2432	-0.0081	0.3591	0.071	0.4577	38.68	-11.7522	38.2769
32	9.2479	1.6192	1.774	4.6544	-1.865	7.0107	-0.0022	-0.0378	-0.4709	0.1175	-0.0414	0.2032	0.5286	-0.3285	0.0288	0.3569	0.2066	0.1439	0.3614	0.0558	0.4471	42.288	-18.0764	43.81
33	6.6282	-0.0085	2.8395	3.781	1.3869	3.2581	-0.1593	-0.5311	0.1316	0.229	0.0635	0.038	-0.0185	0.0602	0.0795	0.2479	0.1773	-0.0434	0.5081	0.1453	0.3626	38.8276	-10.3006	46.8569
34	3.7032	-2.0672	-1.9061	3.429	1.408	3.6576	-0.2144	-0.1339	0.1529	0.2198	-0.1602	-0.245	-0.0261	0.1662	0.0064	0.1898	0.1567	-0.0983	0.408	-0.0174	0.2035	27.6175	-0.636	44.3449

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 47 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 48 through 55 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 56 through 82 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 83 through 92 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 93 through 97 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 98 through 121 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 3 through 15 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 16 through 37 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 38 through 47 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 48 through 55 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 56 through 71 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 72 through 82 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 83 through 91 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 92 through 102 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 103 through 118 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid -1 through 7 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 8 through 38 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 39 through 55 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 56 through 75 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 76 through 82 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 83 through 97 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 98 through 121 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 3 through 7 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 8 through 15 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 16 through 23 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 24 through 38 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 39 through 47 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 48 through 55 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 56 through 75 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 76 through 82 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 83 through 91 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 92 through 102 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 103 through 121 )

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