PDB-4yv9: X-ray crystal structure of Streptococcus dysgalactiae SHP pheromo...

ID or keywords:

Entry

Database: PDB / ID: 4yv9

Title

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

Components

Cyclosporin A
Transcriptional regulator

Keywords

DNA BINDING PROTEIN/INHIBITOR / DNA binding / pheromone binding / repeat domain / quorum sensing / DNA BINDING PROTEIN-INHIBITOR complex

Function / homology

Function and homology information

Biological species

Streptococcus dysgalactiae (bacteria)

Hypocrea pachybasioides (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.95 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_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_auth_evidence / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Apr 2, 2025	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4yv9.cif.gz	489 KB	Display	PDBx/mmCIF format
PDB format	pdb4yv9.ent.gz	409.1 KB	Display	PDB format
PDBx/mmJSON format	4yv9.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4yv9_validation.pdf.gz	518.1 KB	Display	wwPDB validaton report
Full document	4yv9_full_validation.pdf.gz	540.4 KB	Display
Data in XML	4yv9_validation.xml.gz	56 KB	Display
Data in CIF	4yv9_validation.cif.gz	74.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yv/4yv9 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/4yv9	HTTPS FTP

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Related structure data

Related structure data	4yv6C C: citing same article (ref.)
Similar structure data	5iw8-d 5w4n-d 5iwc-d 5o4i-2 6j28-2 6j27-2 2683 6m8r-1 5o4q-3 1y5y-d 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

E: Cyclosporin A

F: Cyclosporin A

G: Cyclosporin A

H: Cyclosporin A

hetero molecules

141 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Transcriptional regulator

B: Transcriptional regulator

E: Cyclosporin A

F: Cyclosporin A

hetero molecules

defined by author&software
Evidence: gel filtration
70.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Transcriptional regulator

D: Transcriptional regulator

G: Cyclosporin A

H: Cyclosporin A

hetero molecules

defined by author&software
Evidence: gel filtration
70.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.388, 99.427, 99.882
Angle α, β, γ (deg.)	90.00, 97.00, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

TETRAMER BY GEL FILTRATION

#1: Protein	Transcriptional regulator Mass: 33731.559 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: Protein/peptide	Cyclosporin A Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1220.625 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI. Source: (synth.) Hypocrea pachybasioides (fungus) / References: NOR: NOR00033, Cyclosporin A
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H₂O
Compound details	CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)
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: 2.41 Å³/Da / Density % sol: 48.98 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: CsA, Tris-HCl (pH 8.0), sodium phosphate, NaCl, DTT, DMSO, Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. obs: 96464 / % possible obs: 99.8 % / Redundancy: 7.39 % / R_sym value: 0.078 / Net I/σ(I): 45.25
Reflection shell	Resolution: 1.95→1.98 Å / R_sym value: 0.66 / % possible all: 100

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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:

SAD / Resolution: 1.95→39.14 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2132	1998	2.07 %
R_work	0.1883	-	-
obs	0.1888	96409	99.74 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→39.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9217	0	65	589	9871

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	9455
X-RAY DIFFRACTION	f_angle_d	1.05	12762
X-RAY DIFFRACTION	f_dihedral_angle_d	14.657	3500
X-RAY DIFFRACTION	f_chiral_restr	0.046	1432
X-RAY DIFFRACTION	f_plane_restr	0.004	1583

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 (%)
1.95-1.9982	0.3196	142	0.2715	6695	X-RAY DIFFRACTION	100
1.9982-2.0522	0.3209	141	0.2526	6662	X-RAY DIFFRACTION	100
2.0522-2.1126	0.2835	144	0.2334	6792	X-RAY DIFFRACTION	100
2.1126-2.1808	0.2622	142	0.2077	6701	X-RAY DIFFRACTION	100
2.1808-2.2587	0.233	142	0.1991	6746	X-RAY DIFFRACTION	100
2.2587-2.3491	0.2439	143	0.1913	6766	X-RAY DIFFRACTION	100
2.3491-2.456	0.2451	143	0.1886	6725	X-RAY DIFFRACTION	100
2.456-2.5855	0.2515	142	0.1944	6722	X-RAY DIFFRACTION	100
2.5855-2.7474	0.2481	144	0.1937	6799	X-RAY DIFFRACTION	100
2.7474-2.9595	0.1974	143	0.1968	6739	X-RAY DIFFRACTION	100
2.9595-3.2572	0.2366	143	0.1991	6780	X-RAY DIFFRACTION	100
3.2572-3.7282	0.2164	142	0.1844	6751	X-RAY DIFFRACTION	100
3.7282-4.6959	0.1684	145	0.1554	6828	X-RAY DIFFRACTION	100
4.6959-39.1493	0.1764	142	0.1867	6705	X-RAY DIFFRACTION	97

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	7.8045	-1.1513	2.4848	3.2684	4.007	8.4047	0.262	-0.9389	-0.4192	0.9058	-0.3543	-2.1485	0.3928	0.6933	-0.018	0.7324	-0.2645	-0.1007	0.7852	0.277	1.0668	16.9498	-32.2617	71.2164
2	7.1489	0.7136	-2.3025	7.7147	-4.2209	7.5307	-0.2774	-0.4163	-0.3784	0.2521	-0.0321	-1.0741	-0.046	0.5553	0.3223	0.4266	-0.0627	-0.004	0.5222	-0.1583	0.5775	17.8923	-24.7634	68.7835
3	5.5582	1.2832	-0.8458	5.1248	4.8312	5.3653	-0.0496	0.0203	-0.2384	-0.6667	-0.1529	0.8261	-0.3929	-0.3726	0.1717	0.4789	-0.0876	0.0201	0.6082	-0.1819	0.5439	6.5592	-20.4508	71.8059
4	2.84	-0.1157	-0.6507	3.892	-0.996	5.169	0.0081	-0.2834	-0.1822	0.2395	-0.0511	0.1993	-0.0045	-0.1925	0.0302	0.1424	-0.0456	-0.0236	0.2617	0.0093	0.2103	-2.1555	-3.3725	88.2386
5	4.701	-2.8335	-0.1706	5.4938	1.7136	5.9116	-0.0271	0.2015	0.0849	-0.344	-0.0263	-0.1322	-0.2726	0.0246	0.024	0.1894	-0.093	-0.0182	0.2018	0.0203	0.2251	-2.0468	2.4349	72.938
6	4.4023	0.0364	0.9968	4.247	-0.2025	3.7484	-0.033	0.1398	0.1353	-0.262	0.088	0.1748	-0.3525	-0.3905	-0.0633	0.3229	-0.0035	-0.0185	0.2753	0.0409	0.1689	-14.4044	0.8293	64.2054
7	4.7376	0.2308	0.7788	2.6501	-1.0207	7.1635	-0.0426	-0.0957	0.1622	0.5163	0.1757	0.5408	-0.7449	-1.1874	-0.0795	0.3693	0.0698	0.0132	0.5607	0.049	0.2746	-27.3015	-4.7679	71.9181
8	7.1785	0.0413	-0.5354	7.13	1.0285	5.1592	-0.0398	1.4383	0.0796	-0.4257	0.1637	-0.3433	0.326	0.8411	-0.1304	0.2718	-0.0185	0.0174	0.6189	-0.0491	0.3561	22.4798	-4.6573	74.1041
9	4.0177	2.4253	0.8084	8.5266	3.6085	7.5316	-0.059	0.9212	-0.6368	-0.7896	-0.0561	0.2183	0.3621	0.1543	0.1328	0.3478	0.0125	-0.0184	0.5325	-0.1493	0.4046	13.1952	-11.6911	70.9604
10	2.5989	1.5441	-0.1257	4.5339	-0.7625	1.8351	-0.4384	0.6042	1.0716	-1.2333	0.4759	0.7901	-0.8922	0.1052	0.1121	1.477	-0.7471	-0.3466	0.3556	0.1613	0.735	1.6306	-21.3081	49.9474
11	4.0332	0.3476	1.5708	3.8233	-0.3896	6.089	-0.2544	0.7901	-0.0353	-0.9383	0.121	0.0672	-0.8152	0.734	0.062	0.6998	-0.2289	0.04	0.3834	-0.0888	0.324	0.8877	-34.306	49.3115
12	6.0326	-0.3041	-0.1465	4.7863	0.2438	3.544	-0.2001	-0.505	-0.3122	0.1552	-0.0156	0.3214	0.6132	-0.3238	0.0069	0.4214	-0.2239	-0.0012	0.2675	0.0088	0.2647	-5.6253	-33.121	64.4035
13	4.3316	-1.1522	-0.5832	4.4238	-0.8579	1.7509	-0.0052	-0.0915	-0.4837	-0.1461	0.1756	0.2734	0.5737	-0.433	-0.1012	0.4208	-0.1982	-0.0699	0.4161	0.0796	0.3192	-17.9672	-27.5349	66.7903
14	5.0399	1.1401	-0.4465	4.3936	0.1563	2.9804	-0.2626	0.2143	-0.5804	-0.5804	0.368	0.5455	0.7527	-1.2915	-0.0282	0.4273	-0.2086	-0.0949	0.6124	0.0206	0.2883	-28.3703	-20.3034	57.2477
15	9.0129	-1.3205	2.143	8.5955	-1.3022	8.4764	0.5089	-0.5739	-1.0645	0.3857	-0.3742	-0.4846	1.0613	0.1309	-0.0535	0.5428	-0.042	-0.1204	0.3581	0.0533	0.4319	24.452	26.4774	83.4105
16	9.6769	4.414	-3.3503	5.5361	-4.0913	3.1238	-0.4954	0.284	-0.7121	-0.465	0.1739	-0.2482	0.7228	0.0058	0.2962	0.3348	-0.0062	0.039	0.3579	-0.0217	0.328	9.7736	40.0457	101.2084
17	7.5867	2.2426	0.8881	6.678	-1.4846	5.2083	0.0121	-0.2169	0.245	0.4627	-0.1064	0.4003	-0.2471	-0.4981	0.0366	0.2393	0.0668	0.0359	0.3096	-0.0448	0.2188	4.9831	47.4413	109.9415
18	5.4368	-0.3637	2.4903	3.9506	-0.8005	3.8468	-0.2281	0.3754	0.7253	0.0751	0.1144	-0.1167	-0.415	0.0966	0.0792	0.2139	-0.0134	-0.0174	0.2001	0.0865	0.3551	7.5032	57.6228	93.8097
19	4.4989	0.7929	0.485	7.594	2.0088	7.2025	-0.317	0.8317	1.707	-0.4949	-0.0631	0.1033	-1.065	-0.6653	0.3101	0.4589	-0.0688	-0.1666	0.547	0.3038	0.8204	-1.055	65.7398	85.4881
20	5.4441	0.0955	-1.0241	6.8305	-0.1692	5.671	-0.0567	0.6164	0.6262	0.2778	-0.2091	0.3827	-0.5369	-0.2903	0.1998	0.2116	-0.0047	-0.0425	0.3519	0.1023	0.2973	-13.5093	55.4311	86.1297
21	5.3733	-0.1434	3.1322	1.3449	1.4674	3.615	-0.208	-1.2223	0.575	1.6325	0.3851	1.0175	-1.5335	-0.7264	-0.1182	1.6472	0.0288	0.2121	0.5142	0.0912	0.5889	-19.9833	60.6474	95.1077
22	8.1488	-3.2912	3.4155	7.5269	1.1605	7.6336	-0.0811	0.4956	0.387	-0.3872	0.1178	-0.1187	0.0552	0.3801	-0.0121	0.176	-0.1101	0.0237	0.3308	0.0294	0.2982	30.9027	48.0264	93.561
23	7.6172	1.8501	-0.9928	6.3126	1.5579	8.2632	-0.2374	0.4732	-0.3648	-0.456	-0.0275	0.1171	-0.0865	-0.0145	0.2209	0.2461	-0.0186	-0.0114	0.2697	0.005	0.2726	25.4688	42.992	90.1231
24	6.4686	1.5513	4.3601	6.1147	-2.2102	6.777	-0.2358	0.45	0.3616	-0.2145	0.0732	-0.1434	-0.3833	0.4776	0.136	0.3588	0.0064	0.0634	0.3015	-0.0342	0.2153	12.3942	36.7266	63.1618
25	4.2854	-1.2182	0.8225	8.5594	-3.688	1.6622	0.116	0.3845	-0.4307	-0.6109	0.0992	0.1054	0.6585	-0.1944	-0.1522	0.4066	0.0324	-0.0088	0.2879	-0.0801	0.3571	5.9539	24.8057	64.6214
26	6.3056	1.3788	1.131	6.7238	1.7322	3.8226	0.2219	-0.4284	-0.208	0.5392	-0.0294	0.0156	0.6184	-0.1762	-0.0187	0.2926	-0.024	0.023	0.0802	0.0236	0.1461	1.4595	25.8345	74.9564
27	5.3308	-2.4199	-0.661	7.3313	0.2444	3.2639	0.0251	-0.2533	-0.3078	0.0627	-0.1331	0.6871	0.3688	-0.7113	0.0473	0.3418	-0.1031	0.0611	0.3916	-0.0266	0.2477	-10.7535	32.4344	79.805
28	8.0385	1.4654	-0.6542	2.4564	2.8001	4.2453	-0.2169	1.1518	0.0935	-1.3893	0.0219	0.9092	0.042	-0.609	0.277	0.5626	0.0755	-0.1132	0.6898	0.0307	0.3799	-16.7509	45.3934	71.0606
29	6.9516	-0.5258	1.2109	2.1944	3.8084	8.4355	-0.112	0.3002	0.1623	-0.1055	-0.1972	0.1708	0.1304	-0.3592	0.3215	0.3995	-0.0791	-0.0112	0.5289	0.0147	0.5047	-12.4682	-8.6651	79.3578
30	2.4316	-2.4793	-0.2431	3.9965	2.9219	4.8851	0.3203	1.0719	2.3479	-0.9316	-0.5539	-0.0043	-2.3374	-1.071	0.2421	1.1967	0.4212	0.2206	0.9006	0.4135	1.1969	-10.2688	-22.7466	54.8922
31	9.2561	1.3017	0.5233	8.131	0.198	1.9576	0.4528	-0.1717	-0.6566	-0.1494	-0.2489	-0.038	0.675	-1.8231	-0.355	0.6559	-0.012	-0.0761	0.7486	0.008	0.6843	-2.8267	48.6985	96.7542
32	6.1364	-1.5482	-1.4484	8.4124	-2.0283	2.4705	1.1334	0.5375	1.1938	-0.6016	0.1053	0.4919	-1.955	-1.6998	-0.9207	0.7501	0.2065	0.1073	0.6285	0.1986	0.5495	-1.8269	38.8062	69.413

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 5:37)
2	X-RAY DIFFRACTION	2	(chain A and resid 38:57)
3	X-RAY DIFFRACTION	3	(chain A and resid 58:71)
4	X-RAY DIFFRACTION	4	(chain A and resid 72:137)
5	X-RAY DIFFRACTION	5	(chain A and resid 138:174)
6	X-RAY DIFFRACTION	6	(chain A and resid 175:246)
7	X-RAY DIFFRACTION	7	(chain A and resid 247:274)
8	X-RAY DIFFRACTION	8	(chain B and resid 5:43)
9	X-RAY DIFFRACTION	9	(chain B and resid 44:71)
10	X-RAY DIFFRACTION	10	(chain B and resid 72:86)
11	X-RAY DIFFRACTION	11	(chain B and resid 87:137)
12	X-RAY DIFFRACTION	12	(chain B and resid 138:175)
13	X-RAY DIFFRACTION	13	(chain B and resid 176:237)
14	X-RAY DIFFRACTION	14	(chain B and resid 238:274)
15	X-RAY DIFFRACTION	15	(chain C and resid 4:66)
16	X-RAY DIFFRACTION	16	(chain C and resid 70:82)
17	X-RAY DIFFRACTION	17	(chain C and resid 83:123)
18	X-RAY DIFFRACTION	18	(chain C and resid 124:197)
19	X-RAY DIFFRACTION	19	(chain C and resid 198:215)
20	X-RAY DIFFRACTION	20	(chain C and resid 216:268)
21	X-RAY DIFFRACTION	21	(chain C and resid 269:274)
22	X-RAY DIFFRACTION	22	(chain D and resid 4:36)
23	X-RAY DIFFRACTION	23	(chain D and resid 37:67)
24	X-RAY DIFFRACTION	24	(chain D and resid 71:109)
25	X-RAY DIFFRACTION	25	(chain D and resid 110:139)
26	X-RAY DIFFRACTION	26	(chain D and resid 140:173)
27	X-RAY DIFFRACTION	27	(chain D and resid 174:247)
28	X-RAY DIFFRACTION	28	(chain D and resid 248:273)
29	X-RAY DIFFRACTION	29	(chain E and resid 2:11)
30	X-RAY DIFFRACTION	30	(chain F and resid 2:11)
31	X-RAY DIFFRACTION	31	(chain G and resid 2:11)
32	X-RAY DIFFRACTION	32	(chain H and resid 2:11)

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