PDB-5tgn: Crystal structure of protein Sthe_2403 from Sphaerobacter thermophilus

ID or keywords:

Entry

Database: PDB / ID: 5tgn

Title

Crystal structure of protein Sthe_2403 from Sphaerobacter thermophilus

Components

Uncharacterized protein

Keywords

UNKNOWN FUNCTION / GEBA genome / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG

Function / homology

SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / SnoaL-like domain-containing protein

Function and homology information

Biological species

Sphaerobacter thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.001 Å

Authors

Michalska, K. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of protein Sthe_2403 from Sphaerobacter thermophilus
Authors: Michalska, K. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Sep 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 26, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 23, 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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Download

PDBx/mmCIF format	5tgn.cif.gz	187.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5tgn.ent.gz	151.7 KB	Display	PDB format
PDBx/mmJSON format	5tgn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5tgn_validation.pdf.gz	453.7 KB	Display	wwPDB validaton report
Full document	5tgn_full_validation.pdf.gz	456.1 KB	Display
Data in XML	5tgn_validation.xml.gz	20.3 KB	Display
Data in CIF	5tgn_validation.cif.gz	28.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tg/5tgn ftp://data.pdbj.org/pub/pdb/validation_reports/tg/5tgn	HTTPS FTP

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Related structure data

Similar structure data	3oqq-d 6pnt-d 4vgc-3 2ioc-d 3kgb-1 6o88-d 4rem-d 5emv-d 3vgc-3 6zor-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC100748

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	90.178, 66.907, 90.635
Angle α, β, γ (deg.)	90.00, 101.41, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-371- HOH

#1: Protein	Uncharacterized protein Mass: 12204.464 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / S 6022 / Gene: Sthe_2403 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Magic / References: UniProt: D1C7H4
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.77 Å³/Da / Density % sol: 55.54 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Bis-Tris propane:NaOH, pH 7, 0.6 M K/Na tartrate, cryo 25% glycerol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97929 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 5, 2011 / Details: mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97929 Å / Relative weight: 1
Reflection	Resolution: 2→30 Å / Num. obs: 35690 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / R_merge(I) obs: 0.096 / Net I/σ(I): 26.88
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 11.3 % / R_merge(I) obs: 0.96 / Mean I/σ(I) obs: 2.75 / CC_1/2: 0.822 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2386)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.001→28.628 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2049	1815	5.1 %	random
R_work	0.1609	-	-	-
obs	0.163	35618	99.54 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.001→28.628 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3337	0	34	226	3597

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3479
X-RAY DIFFRACTION	f_angle_d	0.94	4729
X-RAY DIFFRACTION	f_dihedral_angle_d	20.938	2067
X-RAY DIFFRACTION	f_chiral_restr	0.065	522
X-RAY DIFFRACTION	f_plane_restr	0.007	631

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 (%)
2.0013-2.0554	0.311	138	0.2227	2423	X-RAY DIFFRACTION	94
2.0554-2.1158	0.2799	158	0.2101	2576	X-RAY DIFFRACTION	100
2.1158-2.1841	0.2618	138	0.1942	2603	X-RAY DIFFRACTION	100
2.1841-2.2621	0.2102	144	0.1744	2597	X-RAY DIFFRACTION	100
2.2621-2.3527	0.2368	115	0.1739	2626	X-RAY DIFFRACTION	100
2.3527-2.4597	0.2137	144	0.1643	2593	X-RAY DIFFRACTION	100
2.4597-2.5893	0.2153	143	0.1652	2613	X-RAY DIFFRACTION	100
2.5893-2.7514	0.2261	161	0.1684	2578	X-RAY DIFFRACTION	100
2.7514-2.9636	0.2173	130	0.1694	2623	X-RAY DIFFRACTION	100
2.9636-3.2615	0.2136	129	0.1556	2613	X-RAY DIFFRACTION	100
3.2615-3.7326	0.1872	148	0.145	2623	X-RAY DIFFRACTION	100
3.7326-4.6993	0.159	128	0.1388	2653	X-RAY DIFFRACTION	100
4.6993-28.6314	0.1739	139	0.153	2682	X-RAY DIFFRACTION	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	2.4614	-2.1564	1.1856	8.3886	-1.894	7.3977	-0.0002	-0.8272	0.7379	0.6474	-0.0093	0.2448	-0.8189	-0.1464	0.0449	0.271	-0.017	0.0164	0.272	-0.0473	0.2652	-7.4311	43.7025	34.1523
2	1.2035	-1.509	-0.0591	4.9772	3.9437	7.0629	-0.1195	-0.2236	-0.0975	0.117	0.1021	-0.0484	-0.104	0.1935	0.0719	0.1556	-0.0318	0.0207	0.1787	0.0311	0.108	-7.5219	32.037	35.0547
3	4.6966	-4.4167	-4.3838	4.1742	4.1012	4.1199	-0.049	-0.1665	-0.4289	0.3023	0.0133	0.3956	0.1221	-0.3161	0.2965	0.1937	-0.0639	0.0161	0.269	-0.0052	0.1559	-8.9004	24.2037	32.1537
4	6.9971	2.3475	-3.4102	3.8877	-3.3256	3.1904	0.0695	-0.5196	0.2073	0.2939	-0.0358	-0.0999	-0.2437	0.172	-0.0079	0.2154	-0.0499	-0.0284	0.1975	-0.0409	0.101	-0.3763	32.2038	34.1855
5	5.1355	4.8306	-5.8789	4.6493	-5.3358	9.0682	0.484	0.6474	1.552	-0.3332	0.2507	0.5444	-0.8752	-0.8533	-0.8785	0.4078	0.065	0.0856	0.3141	0.0253	0.4965	-11.8282	45.9915	24.2024
6	6.3298	-5.566	-3.1651	5.711	1.7304	2.9399	0.3384	0.1106	0.0648	-0.2759	-0.1069	-0.3106	-0.1925	-0.0539	-0.2141	0.191	-0.0402	-0.0113	0.1103	0.0166	0.1278	1.0634	38.6145	22.2265
7	6.406	-0.3414	-1.0574	6.1378	1.3964	7.2388	-0.0701	0.2494	0.0824	-0.1483	-0.0953	0.0991	-0.0242	-0.4221	0.1434	0.1507	0.0007	-0.034	0.1199	0.0168	0.0891	-9.8443	35.957	25.802
8	6.1778	-3.9536	-1.6757	5.4679	2.1197	2.7222	-0.443	-1.0159	-1.3211	0.742	0.1203	0.1115	0.7637	0.1994	0.2561	0.4365	0.003	0.0839	0.2612	0.1656	0.4842	2.9745	4.7202	31.4942
9	3.7609	5.0423	0.8927	7.8441	3.5081	9.8315	0.0068	-0.7933	-0.2838	0.7104	-0.0263	0.238	-0.0261	-0.8431	0.0324	0.3626	0.0411	0.0025	0.3789	0.1621	0.2739	1.9113	12.7421	37.8535
10	1.725	-1.0208	-2.4106	7.1378	-0.3993	4.4903	-0.0165	-0.2856	0.0638	0.3132	-0.1483	-0.5521	-0.1137	0.5806	0.1726	0.1302	-0.0498	-0.0386	0.2186	0.0453	0.1692	4.9908	23.1715	30.5303
11	5.545	-0.9628	4.0653	5.6044	-0.2596	3.5201	-0.1583	-0.824	-0.7117	0.8536	0.1476	0.3245	0.521	-0.1288	-0.088	0.238	-0.0263	0.0226	0.3278	0.112	0.2047	-1.1332	17.9657	36.6419
12	9.1802	-7.2924	-7.0065	5.8334	5.6113	5.3934	-0.3246	0.3688	-1.4956	0.0601	-0.6457	1.3598	0.5178	-0.261	0.8721	0.3488	0.0145	0.0025	0.2593	0.009	0.4538	-6.6485	10.4379	23.9426
13	3.1914	2.5492	2.1474	2.0539	1.5954	3.0621	0.6648	0.0417	-1.3524	-0.3993	-0.5321	-0.9028	1.687	0.8656	-0.6721	0.5587	0.1169	-0.0491	0.4506	0.0928	0.7313	11.9347	3.7796	23.0834
14	7.6083	-8.1398	2.2071	8.867	-3.0444	3.2328	0.0698	0.2674	-0.8078	-0.2619	-0.0707	0.495	0.082	0.0601	-0.0215	0.2092	0.0131	0.0174	0.1427	-0.0255	0.2421	-3.3973	11.6335	19.5789
15	8.6469	-4.6764	5.9498	6.1833	-5.0468	9.1804	-0.0545	0.1257	-0.5661	0.1979	0.0752	-0.2039	-0.0388	0.6087	-0.129	0.218	0.0137	0.0085	0.1912	0.0348	0.2651	6.6559	11.8955	24.399
16	6.7774	0.0422	-0.501	8.4153	-1.3169	1.9904	0.0892	0.3621	-0.1677	-0.0669	-0.2923	-0.3096	0.4837	0.7988	0.1117	0.1867	0.0229	0.0273	0.1901	0.0356	0.1819	6.7564	14.474	25.758
17	7.2218	3.3424	-4.5997	8.2785	3.4532	8.6498	-0.1387	0.4557	-0.1809	-0.4202	-0.1782	0.5223	0.2112	-0.7861	0.2904	0.1992	-0.0508	-0.0851	0.3135	0.015	0.1671	-25.3108	23.902	7.8782
18	1.6662	-1.4888	-0.1278	1.9782	-0.3568	5.5408	-0.0767	0.2296	-0.1933	-0.0925	0.0027	0.1373	0.1806	0.0072	0.0841	0.1453	-0.0397	-0.0235	0.1668	-0.0364	0.1499	-14.7879	23.1129	10.9811
19	6.6731	4.9876	-3.4886	4.9167	-0.7632	4.89	-0.3188	0.3222	0.8183	0.2628	0.5257	1.459	-1.1295	-1.5024	-0.3252	0.4199	0.0902	0.0416	0.4508	-0.0178	0.5521	-28.8781	33.3131	19.4083
20	5.5189	0.1745	0.1084	5.7541	-2.3334	6.4378	-0.007	0.1894	-0.3976	0.1687	0.0245	0.2361	-0.3158	-0.1308	0.0065	0.0933	-0.0357	0.0093	0.1518	-0.0467	0.1559	-20.3841	24.3078	18.5249
21	7.7141	0.7304	1.6516	5.9544	-0.3774	7.6498	-0.0533	0.3517	0.0395	-0.3106	-0.024	-0.6149	-0.215	0.6755	0.0897	0.1608	0.0266	0.0258	0.217	-0.001	0.1653	22.6601	26.5361	10.1518
22	4.4944	-1.8473	-0.4895	3.8707	-0.6472	3.8468	0.1968	0.1098	0.2949	0.1038	-0.1242	-0.2274	-0.319	0.2229	-0.0729	0.148	-0.0349	-0.0052	0.158	0.0211	0.1375	12.9674	29.6123	14.2686
23	5.1493	-1.3803	-0.4917	5.4324	2.5351	5.7922	-0.0318	-0.068	0.1431	0.2986	0.13	-0.393	0.4362	0.3664	-0.0802	0.1455	-0.0048	-0.0291	0.1838	0.0714	0.1886	19.3266	24.69	22.0378

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 37 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 38 through 42 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 43 through 59 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 60 through 69 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 70 through 84 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 85 through 108 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 15 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 16 through 30 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 31 through 42 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 43 through 51 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 52 through 61 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 62 through 69 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 70 through 84 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 85 through 94 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 95 through 108 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 1 through 25 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 26 through 61 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 62 through 69 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 70 through 107 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 0 through 30 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 31 through 61 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 62 through 108 )

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