PDB-4yv6: X-ray crystal structure of Streptococcus dysgalactiae SHP pheromo...

ID or keywords:

Entry

Database: PDB / ID: 4yv6

Title

X-ray crystal structure of Streptococcus dysgalactiae SHP pheromone receptor Rgg2

Components

Transcriptional regulator

Keywords

DNA BINDING PROTEIN / DNA binding / pheromone binding / repeat domain / quorum sensing

Function / homology

Function and homology information

Biological species

Streptococcus dysgalactiae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.053 Å

Authors

Neiditch, M.B. / Parashar, V.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Rgg protein structure-function and inhibition by cyclic peptide compounds.
Authors: Parashar, V. / Aggarwal, C. / Federle, M.J. / Neiditch, M.B.

History

Deposition	Mar 19, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 22, 2015	Group: Database references
Revision 1.2	May 6, 2015	Group: Database references
Revision 1.3	Nov 1, 2017	Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Nov 20, 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 / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4yv6.cif.gz	643.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4yv6.ent.gz	549.5 KB	Display	PDB format
PDBx/mmJSON format	4yv6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4yv6_validation.pdf.gz	471.1 KB	Display	wwPDB validaton report
Full document	4yv6_full_validation.pdf.gz	479.6 KB	Display
Data in XML	4yv6_validation.xml.gz	38.7 KB	Display
Data in CIF	4yv6_validation.cif.gz	54.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yv/4yv6 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/4yv6	HTTPS FTP

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Related structure data

Related structure data	4yv9C C: citing same article (ref.)
Similar structure data	5w4n-d 4yv9-2 3ha0-3 3h9y-1 4yv9-1 3kw8-1 5w4m-d 2axz-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	#144 - Dec 2011 Complex I similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (5)

Deposited unit

A: Transcriptional regulator

B: Transcriptional regulator

C: Transcriptional regulator

D: Transcriptional regulator

hetero molecules

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

1

A: Transcriptional regulator

B: Transcriptional regulator

hetero molecules

defined by author&software
Evidence: gel filtration
67.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Transcriptional regulator

D: Transcriptional regulator

hetero molecules

defined by author&software
Evidence: gel filtration
67.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.103, 99.076, 99.895
Angle α, β, γ (deg.)	90.00, 97.03, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

Dimer by Gel filtration

#1: Protein	Transcriptional regulator Mass: 33543.980 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus dysgalactiae (bacteria) / Strain: LT1 / Gene: mutR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J9X288*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Source details	MOLECULE-1 IS FROM A CLINICAL STRAIN KNOWN AS LT1

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.66 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: Tris-HCl (pH 8.0), sodium phosphate (pH 8.0), NaCl, DTT, 2.4 M Ammonium sulfate, and Tris-HCl (pH 8.6)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 2.05→50 Å / Num. obs: 87750 / % possible obs: 99.7 % / Redundancy: 3.68 % / R_sym value: 0.061 / Net I/σ(I): 29.68
Reflection shell	Resolution: 2.05→2.09 Å / R_sym value: 0.53 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.053→39.956 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.243	1870	2.43 %
R_work	0.2078	-	-
obs	0.2086	77046	93.77 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.053→39.956 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8880	0	35	334	9249

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	9085
X-RAY DIFFRACTION	f_angle_d	0.523	12235
X-RAY DIFFRACTION	f_dihedral_angle_d	12.77	3387
X-RAY DIFFRACTION	f_chiral_restr	0.024	1360
X-RAY DIFFRACTION	f_plane_restr	0.001	1511

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 (%)
2.053-2.1088	0.4048	115	0.3463	4840	X-RAY DIFFRACTION	79
2.1088-2.1708	0.3137	125	0.322	5192	X-RAY DIFFRACTION	85
2.1708-2.2409	0.3664	128	0.2923	5423	X-RAY DIFFRACTION	88
2.2409-2.321	0.3005	145	0.2706	5550	X-RAY DIFFRACTION	90
2.321-2.4139	0.2675	146	0.2495	5681	X-RAY DIFFRACTION	93
2.4139-2.5237	0.2644	142	0.2383	5830	X-RAY DIFFRACTION	95
2.5237-2.6568	0.2677	145	0.2366	5887	X-RAY DIFFRACTION	96
2.6568-2.8232	0.2457	153	0.2281	6008	X-RAY DIFFRACTION	97
2.8232-3.0411	0.2482	153	0.2224	6053	X-RAY DIFFRACTION	99
3.0411-3.347	0.2423	153	0.2168	6159	X-RAY DIFFRACTION	99
3.347-3.831	0.2498	155	0.1914	6160	X-RAY DIFFRACTION	100
3.831-4.8253	0.2044	156	0.1598	6201	X-RAY DIFFRACTION	100
4.8253-39.9634	0.2135	154	0.1867	6192	X-RAY DIFFRACTION	98

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	0.0014	-0.1362	0.0078	0.1961	-0.127	0.0991	0.0035	0.4493	-1.2102	-0.7936	0.3606	1.4543	0.8234	-0.605	0.0166	0.6732	0.2145	-0.0918	0.8742	-0.2025	0.9951	-31.9209	15.1121	78.1341
2	0.7802	-1.403	-0.993	1.8796	0.5953	0.7951	0.2021	0.3298	-0.0868	-0.2577	-0.3777	0.3943	0.2568	-0.0208	-0.0001	0.6395	0.0848	-0.0149	0.6927	0.1753	0.7308	-35.0482	23.1675	78.684
3	1.629	-0.2376	-0.3139	2.925	0.0623	2.3248	0.0459	0.4048	-0.1184	-0.2178	-0.2181	-0.3012	0.1137	0.1329	-0.0002	0.3093	0.0395	0.0326	0.3785	-0.0202	0.395	-14.6475	42.2825	58.6013
4	0.1232	0.0826	-0.1132	0.0463	-0.0411	0.1067	-0.1568	0.1852	1.2246	-0.4422	-0.16	0.9484	-2.2316	-0.5112	0.002	0.5267	-0.0074	0.0075	0.3992	-0.0465	0.541	-16.8628	58.3762	60.6335
5	3.1236	0.2404	1.0155	1.8778	0.3226	2.8113	-0.0518	-0.0872	0.0558	0.1637	-0.0549	0.0556	-0.2364	0.0507	-0	0.3178	0.0158	0.0456	0.2548	-0.0204	0.3059	-13.1666	51.4547	78.7831
6	2.183	-1.0605	0.4492	3.6762	0.4837	2.8314	-0.1559	0.1043	0.1113	0.1487	0.1258	-0.3779	-0.1857	0.863	0	0.3828	-0.0349	0.0011	0.5803	-0.0354	0.351	4.9112	45.2726	82.6467
7	0.1757	0.1789	-0.0112	0.1174	-0.0283	0.2046	0.3252	1.116	-0.2038	-0.8977	0.0495	0.0327	-0.3896	0.9306	0.0002	0.6669	-0.298	0.0666	0.9495	-0.0134	0.4837	10.3433	52.0937	74.1717
8	2.5686	-0.5414	-0.3646	3.1516	-0.7088	1.5496	-0.0683	-0.7379	-0.3098	0.3383	0.0587	0.082	0.0802	-0.4111	-0.0001	0.3821	-0.0188	0.0001	0.6812	0.06	0.4854	-36.9458	41.3909	75.915
9	1.0852	0.1052	0.7728	0.6957	-0.046	1.0487	-0.7562	-1.5776	0.5811	0.5471	0.3282	-0.1556	-1.2606	-1.2773	-0.0022	1.1312	0.3125	-0.1621	0.6323	-0.1037	0.6324	-19.3262	27.5168	99.7715
10	0.568	0.8784	0.1047	1.5667	0.071	0.0335	-0.5531	-0.8438	0.7684	0.7335	-0.4552	1.9725	-0.2673	0.8204	-0.032	1.3331	0.6224	0.3083	1.1048	0.0861	0.5639	-23.0942	21.5092	107.3826
11	1.8255	-0.6728	0.2786	1.4818	-0.804	1.0509	-0.1799	-0.3619	-0.4119	0.5158	0.0021	0.0596	0.06	-0.182	-0	0.6797	0.1724	0.0387	0.4001	0.0795	0.4974	-17.4954	13.9776	94.3138
12	2.2351	1.5639	-0.7165	2.054	0.6317	1.3029	-0.0724	0.2692	-0.1574	-0.0895	0.1879	-0.0828	0.3263	0.1066	0.0001	0.5118	0.167	-0.0266	0.423	-0.0763	0.4506	-8.2931	19.0942	81.8542
13	0.8679	-0.2389	-0.2628	1.0231	0.7695	0.6405	-0.055	-0.0687	-0.2182	-0.2555	0.242	-0.2931	0.7609	0.4958	-0.0097	0.6486	0.223	-0.0425	0.5998	-0.1404	0.6191	1.4196	15.7397	79.5996
14	2.2658	0.3972	-0.0108	2.7783	0.7976	1.5375	-0.0282	0.0297	-0.4323	0.3336	0.2119	-0.2467	0.372	0.611	-0	0.4822	0.1712	-0.0534	0.6067	-0.0659	0.4624	7.956	27.6057	88.1895
15	0.4755	0.0311	0.579	1.3467	-0.4837	0.5377	1.1465	0.1671	-1.24	-0.2995	-0.136	0.7363	1.5347	-0.4573	0.0077	0.9242	0.0454	-0.3323	0.794	-0.0676	0.9085	-43.6754	71.7805	66.7892
16	0.0175	-0.012	-0.0322	0.0559	0.0262	0.0216	0.8094	0.0925	0.116	0.0744	0.2454	-0.4013	0.62	0.9067	-0.0004	1.2237	0.0282	-0.2222	0.8542	-0.1626	0.8688	-48.6352	72.5332	58.2681
17	0.2996	0.1639	0.4831	0.7362	0.1115	0.73	0.7309	0.0588	-0.1715	-0.3451	-0.4826	-0.173	-0.1669	0.1008	0.0003	0.5788	0.0698	-0.0512	0.6174	0.0502	0.4598	-39.0172	80.8659	65.4194
18	1.6718	-0.3656	-0.4921	2.2323	0.9956	1.5257	-0.2032	0.1324	-0.0664	0.0346	-0.0276	0.0294	-0.0272	0.3807	0	0.3847	-0.0115	0.0259	0.6054	0.0198	0.4105	-24.8688	92.9301	41.4308
19	1.6502	0.3813	0.496	2.2563	0.1624	0.7437	-0.3686	0.4008	0.5874	-0.2597	0.118	0.0397	-0.457	0.2083	-0	0.4824	-0.0475	-0.1156	0.3884	0.0514	0.5844	-26.4726	107.2149	48.0371
20	3.53	-0.6225	1.5385	2.4064	1.2126	2.4463	-0.2046	-0.7296	0.7103	-0.0276	0.0147	0.2244	-0.3045	-0.0568	-0.0056	0.395	0.0651	-0.0218	0.4014	-0.1675	0.5201	-17.1232	107.3684	63.1586
21	2.5666	-0.6599	-0.0343	1.3534	-0.076	1.351	-0.1704	-0.2002	0.5523	-0.4612	0.073	-0.4812	-0.4822	0.476	-0.0001	0.4871	-0.0537	0.0645	0.4999	-0.0627	0.5474	-0.5224	104.3061	58.8335
22	1.5127	0.4323	0.2432	0.9354	-0.6609	0.6424	-0.1707	-0.3719	0.2219	0.0675	0.0675	-0.0227	0.0394	-0.2992	-0	0.3729	0.0644	0.0021	0.602	-0.0729	0.4769	-49.7525	97.0051	55.4598
23	0.772	-0.9598	0.0387	1.365	-0.5994	0.752	0.0523	-0.2684	-0.5225	0.2662	-0.1221	-0.2095	0.2754	0.2042	0.0001	0.4668	-0.017	0.0074	0.5269	-0.0229	0.4977	-42.1184	90.7664	57.5338
24	1.9978	-0.2525	0.2965	1.6367	1.4369	2.916	0.0615	-0.354	0.0416	0.1257	0.0197	0.0422	-0.1239	-0.3066	0	0.5199	-0.0667	0.0248	0.3893	0.0366	0.4025	-27.8453	80.8437	85.9053
25	2.2209	0.4208	-0.634	1.7933	-0.6373	0.2764	0.1393	0.2986	-0.1005	-0.3557	-0.0732	0.12	0.4587	-0.0468	0.0001	0.482	0.0398	-0.0055	0.2958	-0.0179	0.339	-20.2367	74.5135	72.8365
26	1.9074	1.5298	-0.6084	3.3805	1.031	1.085	0.2474	0.2613	0.0994	-0.0267	-0.1091	-0.4281	0.5539	0.2785	0.0002	0.4788	0.0848	0.0153	0.4266	0.0204	0.4001	-11.9437	79.4311	70.8271
27	0.5861	1.0358	-0.1905	2.2704	0.4515	0.9315	0.0013	0.0226	-0.2631	-0.1858	-0.1173	-0.4437	0.4981	0.3337	0.0019	0.4337	0.1221	0.075	0.5432	0.0801	0.4939	-5.3898	81.6736	66.8394
28	0.832	0.6455	0.1253	1.3299	-0.1238	1.4591	-0.2255	-0.44	-0.0805	0.547	0.1935	-0.774	0.287	0.2585	-0	0.6113	0.0476	-0.0783	0.7982	-0.0087	0.5968	1.231	91.9588	76.0838

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 6:28)
2	X-RAY DIFFRACTION	2	(chain A and resid 29:71)
3	X-RAY DIFFRACTION	3	(chain A and resid 72:122)
4	X-RAY DIFFRACTION	4	(chain A and resid 123:127)
5	X-RAY DIFFRACTION	5	(chain A and resid 128:216)
6	X-RAY DIFFRACTION	6	(chain A and resid 217:266)
7	X-RAY DIFFRACTION	7	(chain A and resid 267:274)
8	X-RAY DIFFRACTION	8	(chain B and resid 4:70)
9	X-RAY DIFFRACTION	9	(chain B and resid 71:89)
10	X-RAY DIFFRACTION	10	(chain B and resid 90:97)
11	X-RAY DIFFRACTION	11	(chain B and resid 98:156)
12	X-RAY DIFFRACTION	12	(chain B and resid 157:196)
13	X-RAY DIFFRACTION	13	(chain B and resid 197:216)
14	X-RAY DIFFRACTION	14	(chain B and resid 217:274)
15	X-RAY DIFFRACTION	15	(chain C and resid 5:36)
16	X-RAY DIFFRACTION	16	(chain C and resid 37:42)
17	X-RAY DIFFRACTION	17	(chain C and resid 43:66)
18	X-RAY DIFFRACTION	18	(chain C and resid 71:116)
19	X-RAY DIFFRACTION	19	(chain C and resid 117:164)
20	X-RAY DIFFRACTION	20	(chain C and resid 165:237)
21	X-RAY DIFFRACTION	21	(chain C and resid 238:274)
22	X-RAY DIFFRACTION	22	(chain D and resid 5:40)
23	X-RAY DIFFRACTION	23	(chain D and resid 41:65)
24	X-RAY DIFFRACTION	24	(chain D and resid 71:136)
25	X-RAY DIFFRACTION	25	(chain D and resid 137:174)
26	X-RAY DIFFRACTION	26	(chain D and resid 175:202)
27	X-RAY DIFFRACTION	27	(chain D and resid 203:238)
28	X-RAY DIFFRACTION	28	(chain D and resid 239:274)

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