PDB-5u8k: RitR mutant - C128S

ID or keywords:

Entry

Database: PDB / ID: 5u8k

Title

RitR mutant - C128S

Components

Response regulator

Keywords

TRANSCRIPTION / Repressor of iron transporter / Aspartate-less receiver domain protein /

transcription regulator /

monomer

Function / homology

Function and homology information

phosphorelay signal transduction system / regulation of DNA-templated transcription /

Biological species

Streptococcus pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.69 Å

Authors

Silvaggi, N.R. / Han, L.

Citation

Journal: PLoS Pathog. / Year: 2018
Title: RitR is an archetype for a novel family of redox sensors in the streptococci that has evolved from two-component response regulators and is required for pneumococcal colonization.
Authors: Glanville, D.G. / Han, L. / Maule, A.F. / Woodacre, A. / Thanki, D. / Abdullah, I.T. / Morrissey, J.A. / Clarke, T.B. / Yesilkaya, H. / Silvaggi, N.R. / Ulijasz, A.T.

History

Deposition	Dec 14, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 28, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5u8k.cif.gz	296.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5u8k.ent.gz	259.1 KB	Display	PDB format
PDBx/mmJSON format	5u8k.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/u8/5u8k ftp://data.pdbj.org/pub/pdb/validation_reports/u8/5u8k	HTTPS FTP

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Related structure data

Related structure data	5u8mC 5vfaC C: citing same article (ref.)
Similar structure data	4pox-2 6uk1-2 5vfa-1 2qlt-d 5ot8-2 6edk-d 2pzf-2 4j4h-1 1lah-d 3v5j-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	#190 - Oct 2015 Two-component Systems similarity (10) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Response regulator

B: Response regulator

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

1

A: Response regulator

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

2

B: Response regulator

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

Unit cell

Length a, b, c (Å)	141.128, 60.079, 53.324
Angle α, β, γ (deg.)	90.00, 96.00, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Response regulator / Mass: 27438.307 Da / Num. of mol.: 2 / Mutation: C128S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: Hungary19A-6 / Gene: SPH_0483 / Plasmid: pE-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1I9H6
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 690 / 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: 2.05 Å³/Da / Density % sol: 39.95 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion / pH: 8 / Details: 0.1 M ammonium acetate, 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 16, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.69→40.33 Å / Num. obs: 91682 / % possible obs: 99.6 % / Redundancy: 5.6 % / R_merge(I) obs: 0.09 / Net I/σ(I): 16.6
Reflection shell	Resolution: 1.69→1.75 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.34 / Mean I/σ(I) obs: 8.1 / % possible all: 97.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2148: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
autoSHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.69→40.329 Å / SU ML: 0.11 / Cross valid method: NONE / σ(F): 1.84 / Phase error: 15.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1686	3722	4.06 %
R_work	0.1457	-	-
obs	0.1466	91682	93.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.69→40.329 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3776	0	0	690	4466

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3927
X-RAY DIFFRACTION	f_angle_d	1.03	5299
X-RAY DIFFRACTION	f_dihedral_angle_d	14.06	2445
X-RAY DIFFRACTION	f_chiral_restr	0.058	601
X-RAY DIFFRACTION	f_plane_restr	0.006	673

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 (%)
1.6903-1.7117	0.1828	92	0.1591	2237	X-RAY DIFFRACTION	63
1.7117-1.7342	0.1672	114	0.1547	2690	X-RAY DIFFRACTION	79
1.7342-1.758	0.1783	116	0.1594	2785	X-RAY DIFFRACTION	81
1.758-1.7831	0.1739	130	0.1591	2966	X-RAY DIFFRACTION	84
1.7831-1.8097	0.2272	123	0.1545	2906	X-RAY DIFFRACTION	86
1.8097-1.838	0.167	127	0.1447	3099	X-RAY DIFFRACTION	88
1.838-1.8681	0.1628	138	0.1489	3144	X-RAY DIFFRACTION	91
1.8681-1.9003	0.1821	140	0.1446	3214	X-RAY DIFFRACTION	93
1.9003-1.9349	0.171	133	0.1453	3254	X-RAY DIFFRACTION	95
1.9349-1.9721	0.2119	135	0.1389	3347	X-RAY DIFFRACTION	96
1.9721-2.0124	0.1429	141	0.145	3384	X-RAY DIFFRACTION	97
2.0124-2.0561	0.1756	142	0.1407	3389	X-RAY DIFFRACTION	98
2.0561-2.1039	0.1713	147	0.1343	3383	X-RAY DIFFRACTION	99
2.1039-2.1565	0.1716	146	0.1387	3501	X-RAY DIFFRACTION	99
2.1565-2.2149	0.1521	141	0.1364	3422	X-RAY DIFFRACTION	99
2.2149-2.28	0.1681	143	0.1304	3450	X-RAY DIFFRACTION	100
2.28-2.3536	0.161	149	0.1374	3439	X-RAY DIFFRACTION	100
2.3536-2.4377	0.1685	151	0.1341	3508	X-RAY DIFFRACTION	100
2.4377-2.5353	0.168	145	0.1386	3452	X-RAY DIFFRACTION	100
2.5353-2.6507	0.191	142	0.1426	3453	X-RAY DIFFRACTION	100
2.6507-2.7904	0.1997	152	0.1437	3475	X-RAY DIFFRACTION	100
2.7904-2.9652	0.176	145	0.1452	3475	X-RAY DIFFRACTION	100
2.9652-3.194	0.1471	147	0.1479	3438	X-RAY DIFFRACTION	100
3.194-3.5153	0.1539	148	0.1405	3466	X-RAY DIFFRACTION	100
3.5153-4.0235	0.1354	145	0.1387	3430	X-RAY DIFFRACTION	99
4.0235-5.0677	0.1549	150	0.1415	3356	X-RAY DIFFRACTION	98
5.0677-40.3406	0.2012	136	0.2049	3301	X-RAY DIFFRACTION	95

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	2.4031	-0.3215	-0.3009	2.5195	0.498	3.0867	0.0127	-0.1192	0.0822	0.0213	0.0513	0.1629	-0.067	0.0509	-0.0126	0.0203	-0.0116	0.0133	0.0616	0.0207	0.0595	39.2151	49.1501	8.1123
2	2.4558	-0.9213	-0.1303	3.5484	-0.0067	1.7009	-0.0548	-0.0801	-0.3709	0.2407	0.0019	0.365	0.1745	-0.1866	-0.0474	0.1018	-0.0271	-0.0035	0.1091	0.0117	0.0986	40.1176	38.8309	3.345
3	1.7758	-0.1581	0.0256	1.8275	0.6065	1.7204	0.068	-0.0681	0.0106	0.01	-0.0047	-0.0674	0.1382	0.0372	-0.0407	0.0496	-0.0007	0.0037	0.0582	0.0098	0.0307	53.1629	44.0535	4.8203
4	1.809	-0.5357	-0.8347	2.1204	1.472	5.1422	0.0863	0.2326	0.0539	-0.2154	-0.0801	0.1444	-0.0602	-0.1108	0.0145	0.052	0.0046	-0.0197	0.0653	0.0289	0.0846	47.5025	54.5722	-8.1798
5	1.7824	0.2918	-0.2741	1.6699	0.0959	3.2578	-0.0541	0.5962	-0.279	-0.3165	-0.0271	0.2692	-0.0395	-0.2469	-0.0356	0.141	0.0144	-0.036	0.2219	-0.0239	0.1298	57.7036	38.6387	-18.989
6	2.1687	-0.1356	-0.3352	2.1666	-1.0948	1.1874	0.0782	0.1387	0.2523	-0.0531	0.0105	0.0413	-0.0995	-0.0328	0.0038	0.0504	0.0009	-0.006	0.0798	0.0254	0.0485	61.5951	52.4605	-10.7432
7	1.6983	-0.3685	-0.2784	5.1415	0.7623	0.6227	-0.0247	0.1212	0.041	-0.0789	0.026	-0.2563	0.1075	-0.0098	0.0543	0.0338	0.017	-0.0018	0.0755	0.0209	0.0772	73.1262	42.3479	-15.6839
8	3.3535	1.1102	0.1952	5.4218	-0.6924	1.3147	-0.162	0.3724	0.1166	-0.047	0.1394	0.1712	0.1467	0.0043	-0.0942	0.0615	0.0254	0.0071	0.1319	0.0312	0.082	71.9457	50.8663	-18.2643
9	1.9557	0.0401	-0.1624	3.3313	0.2394	2.7341	-0.0306	0.0773	0.0242	-0.1283	0.0431	-0.2516	-0.1686	0.2026	0.1166	0.0299	-0.0324	0.0117	0.1099	-0.0264	0.057	98.1544	15.5705	23.7311
10	3.4618	0.6175	0.3544	0.6927	-0.8464	2.2083	-0.2159	0.2559	-0.0019	-0.0353	0.1212	-0.1197	-0.1262	0.1456	-0.158	0.0312	-0.0506	0.0365	0.1159	-0.0284	0.059	101.1517	21.544	17.36
11	2.3465	1.3102	-0.3565	4.2046	-0.7081	2.1586	-0.0864	-0.0837	-0.5133	-0.1295	0.0367	-0.553	0.204	0.4237	-0.0615	0.0761	0.0163	0.0078	0.136	-0.0122	0.1157	99.7794	9.2673	25.9655
12	2.3039	0.2403	-0.2074	2.0574	-0.3431	2.9469	-0.0116	0.1227	-0.0199	-0.0861	0.0914	0.1716	0.0882	-0.1392	-0.0394	0.05	-0.0166	-0.0067	0.0715	-0.0001	0.0526	86.2251	12.1607	23.1011
13	0.8765	-0.1534	-1.2385	0.9808	-0.2528	6.4439	-0.0574	-0.0239	0.0324	0.1503	-0.0623	-0.0829	-0.0195	0.0209	0.0208	0.0644	-0.0217	-0.0001	0.0482	-0.0181	0.0651	90.147	25.4213	34.1834
14	1.3885	-0.1768	-1.2451	1.4122	0.1859	1.8291	-0.0783	-0.0633	0.2026	0.1203	0.1466	-0.0881	-0.233	0.2069	-0.0419	0.1353	0.0064	-0.0193	0.078	0.0026	0.0978	83.1235	13.857	49.7779
15	1.4634	0.4632	-0.2963	2.8457	-0.8836	1.4871	-0.026	-0.0371	-0.1613	0.0929	-0.0352	-0.1156	0.0604	0.0622	0.0422	0.0455	0.0074	0.0077	0.0724	-0.0071	0.0393	80.3676	11.914	42.4394
16	1.952	0.2699	0.7861	1.8592	-0.2676	3.5707	-0.0309	-0.2983	0.2429	0.1601	0.1277	-0.1091	-0.2961	-0.0297	-0.058	0.0777	0.0172	-0.0092	0.0807	-0.0312	0.0468	74.0012	27.3852	41.3441
17	2.5424	0.7312	-0.7032	2.5084	0.108	2.0322	-0.1036	0.1584	0.0481	-0.4596	0.1132	0.0788	-0.0835	-0.1398	-0.0474	0.0805	0.01	-0.0211	0.0807	-0.023	0.0493	75.1233	20.6065	33.0912
18	2.067	0.5299	0.3186	0.9991	0.2953	2.3872	-0.0589	0.0001	-0.3117	0.1214	-0.0967	0.123	0.2786	-0.0575	0.126	0.1012	-0.0033	0.0606	0.1049	0.0071	0.1463	66.4483	14.8562	44.6671

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 44 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 45 through 106 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 107 through 130 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 131 through 159 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 160 through 208 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 209 through 220 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 221 through 230 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 11 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 12 through 25 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 26 through 44 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 45 through 106 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 107 through 130 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 131 through 147 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 148 through 170 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 171 through 185 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 186 through 208 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 209 through 230 )

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