PDB-2yp6: Crystal structure of the pneumoccocal exposed lipoprotein thiored...

ID or keywords:

Entry

Database: PDB / ID: 2yp6

Title

Crystal structure of the pneumoccocal exposed lipoprotein thioredoxin sp_1000 (Etrx2) from Streptococcus pneumoniae strain TIGR4 in complex with Cyclofos 3 TM

Components

THIOREDOXIN FAMILY PROTEIN

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

oxidoreductase activity
Similarity search - Function

Biological species

STREPTOCOCCUS PNEUMONIAE TIGR4 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.767 Å

Authors

Bartual, S.G. / Shalek, M. / Abdullah, M.R. / Jensch, I. / Asmat, T.M. / Petruschka, L. / Pribyl, T. / Hermoso, J.A. / Hammerschmidt, S.

Citation

Journal: Embo Mol.Med. / Year: 2013
Title: Molecular Architecture of Streptococcus Pneumoniae Surface Thioredoxin-Fold Lipoproteins Crucial for Extracellular Oxidative Stress Resistance and Maintenance of Virulence.
Authors: Saleh, M. / Bartual, S.G. / Abdullah, M.R. / Jensch, I. / Asmat, T.M. / Petruschka, L. / Pribyl, T. / Gellert, M. / Lillig, C.H. / Antelmann, H. / Hermoso, J.A. / Hammerschmidt, S.

History

Deposition	Oct 29, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 30, 2013	Provider: repository / Type: Initial release
Revision 1.1	Dec 11, 2013	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2yp6.cif.gz	245.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2yp6.ent.gz	200.9 KB	Display	PDB format
PDBx/mmJSON format	2yp6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2yp6_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	2yp6_full_validation.pdf.gz	1.4 MB	Display
Data in XML	2yp6_validation.xml.gz	29.8 KB	Display
Data in CIF	2yp6_validation.cif.gz	40.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yp/2yp6 ftp://data.pdbj.org/pub/pdb/validation_reports/yp/2yp6	HTTPS FTP

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Related structure data

Related structure data	4hqsC 4hqzC 2h1bS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6gkq-d 1r2e-d 4ehr-d 2b1k-d 2a0j-d 5ura-2 1af3-d 3pl7-2 6o0l-2 6xvr-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) 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

Related structure data

4hqsC

4hqzC

2h1bS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: THIOREDOXIN FAMILY PROTEIN

B: THIOREDOXIN FAMILY PROTEIN

C: THIOREDOXIN FAMILY PROTEIN

D: THIOREDOXIN FAMILY PROTEIN

hetero molecules

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

1

A: THIOREDOXIN FAMILY PROTEIN

hetero molecules

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

2

B: THIOREDOXIN FAMILY PROTEIN

hetero molecules

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

3

C: THIOREDOXIN FAMILY PROTEIN

hetero molecules

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

4

D: THIOREDOXIN FAMILY PROTEIN

hetero molecules

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

Unit cell

Length a, b, c (Å)	61.460, 116.310, 116.420
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	THIOREDOXIN FAMILY PROTEIN Mass: 20724.902 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE TIGR4 (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97R36, UniProt: A0A0H2UPR5*PLUS
#2: Chemical	ChemComp-C6W / 3-Cyclohexyl-1-Propylphosphocholine Mass: 301.318 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₄NO₄P
#3: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₂O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.8 Å³/Da / Density % sol: 56.03 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.77→32.81 Å / Num. obs: 82391 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / R_merge(I) obs: 0.04 / Net I/σ(I): 37.1
Reflection shell	Resolution: 1.77→1.86 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 4.2 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H1B

2h1b

Resolution: 1.767→32.813 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 18.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1899	4125	5 %
R_work	0.165	-	-
obs	0.1662	82277	99.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.767→32.813 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4536	0	136	423	5095

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	4783
X-RAY DIFFRACTION	f_angle_d	1.302	6439
X-RAY DIFFRACTION	f_dihedral_angle_d	16.573	1843
X-RAY DIFFRACTION	f_chiral_restr	0.078	661
X-RAY DIFFRACTION	f_plane_restr	0.007	830

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 (%)
1.767-1.7878	0.3333	135	0.31	2630	X-RAY DIFFRACTION	98
1.7878-1.8096	0.3568	149	0.2981	2640	X-RAY DIFFRACTION	98
1.8096-1.8325	0.2955	145	0.2825	2638	X-RAY DIFFRACTION	100
1.8325-1.8566	0.2888	135	0.2635	2673	X-RAY DIFFRACTION	100
1.8566-1.8821	0.2841	138	0.231	2671	X-RAY DIFFRACTION	100
1.8821-1.9089	0.2443	145	0.2152	2654	X-RAY DIFFRACTION	100
1.9089-1.9374	0.2363	124	0.2152	2677	X-RAY DIFFRACTION	100
1.9374-1.9677	0.2488	124	0.1965	2684	X-RAY DIFFRACTION	100
1.9677-2	0.2069	145	0.1843	2643	X-RAY DIFFRACTION	100
2-2.0344	0.2139	154	0.1723	2645	X-RAY DIFFRACTION	100
2.0344-2.0714	0.2143	136	0.1681	2681	X-RAY DIFFRACTION	100
2.0714-2.1113	0.2178	165	0.1628	2664	X-RAY DIFFRACTION	100
2.1113-2.1543	0.1892	114	0.1579	2706	X-RAY DIFFRACTION	100
2.1543-2.2012	0.1783	159	0.1573	2671	X-RAY DIFFRACTION	100
2.2012-2.2524	0.1748	137	0.1522	2664	X-RAY DIFFRACTION	100
2.2524-2.3087	0.1659	131	0.143	2692	X-RAY DIFFRACTION	100
2.3087-2.3711	0.1819	155	0.1455	2679	X-RAY DIFFRACTION	100
2.3711-2.4408	0.197	135	0.1539	2695	X-RAY DIFFRACTION	100
2.4408-2.5196	0.2178	148	0.1542	2678	X-RAY DIFFRACTION	100
2.5196-2.6096	0.1924	143	0.1565	2693	X-RAY DIFFRACTION	100
2.6096-2.714	0.1929	154	0.1684	2693	X-RAY DIFFRACTION	100
2.714-2.8375	0.2043	138	0.1717	2733	X-RAY DIFFRACTION	100
2.8375-2.987	0.1901	137	0.1729	2710	X-RAY DIFFRACTION	100
2.987-3.174	0.1523	162	0.1505	2680	X-RAY DIFFRACTION	100
3.174-3.4188	0.1626	152	0.1401	2739	X-RAY DIFFRACTION	100
3.4188-3.7624	0.1458	134	0.1339	2750	X-RAY DIFFRACTION	100
3.7624-4.3058	0.1509	161	0.1311	2729	X-RAY DIFFRACTION	100
4.3058-5.4209	0.1654	133	0.1388	2799	X-RAY DIFFRACTION	100
5.4209-32.8187	0.2098	137	0.2047	2941	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	2.7974	4.9793	2.7428	9.1951	4.0992	4.38	0.0796	-0.0386	0.8601	-0.0886	-0.2292	0.7359	-0.2663	-0.3468	0.0759	0.1663	0.0517	-0.0018	0.1516	-0.0024	0.2821	0.3876	55.2688	44.6737
2	5.7066	2.2409	0.5198	3.5312	2.7558	2.8306	-0.0298	-0.0786	-0.5126	0.4283	-0.3952	0.6291	0.4331	-0.8995	0.3973	0.1952	-0.0575	0.0253	0.3299	-0.0288	0.2504	-6.9329	38.331	41.5824
3	4.1215	-0.4038	-2.7839	5.492	1.281	7.3745	0.0759	-0.21	0.0123	0.2321	-0.0422	0.209	0.0484	-0.1046	0.0634	0.0984	-0.0233	-0.0012	0.0981	-0.0019	0.112	3.5762	43.703	47.7826
4	2.8988	-0.6969	0.7427	2.6849	-0.6433	2.7909	0.0302	0.1865	-0.2812	-0.0902	-0.0629	0.0869	0.2574	0.1516	0.0161	0.1321	0.0104	0.0064	0.1293	-0.009	0.1285	5.5286	35.2961	35.7202
5	2.8353	0.1074	0.203	3.2198	1.0812	3.0728	-0.0445	0.2521	0.2962	-0.1876	0.019	0.0671	-0.3006	0.1223	-0.0241	0.1207	-0.0191	0.0153	0.0977	0.0394	0.1484	6.2112	49.8155	40.2833
6	6.6158	-2.7827	-2.6207	6.9177	4.0205	5.0172	0.0547	-0.4566	0.4609	0.2514	0.1611	-0.7437	-0.2124	0.6522	-0.1576	0.156	-0.0533	-0.0513	0.253	0.0124	0.1896	14.1087	45.1614	51.3023
7	4.9185	-0.2128	-1.7612	3.4778	2.0361	3.3571	-0.0166	-0.2277	0.3259	-0.2379	0.3406	-0.5875	-0.2504	0.6952	-0.1603	0.1316	-0.0179	0.0003	0.18	0.0058	0.2272	49.3733	15.6564	16.5914
8	5.2086	-0.1347	0.6195	1.3348	0.7899	4.2952	0.0233	0.0276	0.3982	-0.0846	0.0352	0.1643	-0.4169	0.1363	0.0252	0.1497	-0.0235	0.0418	0.1012	-0.0072	0.1378	41.051	20.1215	15.4309
9	3.5051	-0.7529	1.1777	3.7695	-3.422	5.6627	-0.0263	-0.0029	-0.2594	-0.2123	0.0929	0.1223	0.2422	-0.3744	-0.025	0.1596	-0.0309	-0.0434	0.0915	-0.009	0.14	33.7271	6.8423	9.0649
10	3.3816	-1.0504	0.5931	2.199	-0.8496	2.002	0.0646	0.1033	0.0997	-0.3368	0.025	0.3661	-0.3011	0.0155	-0.0185	0.1752	0.0114	-0.0162	0.0939	0.0147	0.1219	40.9194	12.1132	10.2629
11	1.9602	1.563	2.0289	4.1438	1.8701	2.1558	0.2085	0.8636	-0.5099	-0.7016	-0.2925	-0.25	0.7742	0.8245	-0.1322	0.3324	0.1304	0.0228	0.2742	-0.0152	0.1779	44.3187	1.4354	1.7266
12	3.7481	-0.7425	0.5038	3.6771	0.0153	3.7345	-0.0797	0.3953	0.0383	-0.2252	0.0286	-0.033	-0.1091	0.2575	0.0359	0.1234	-0.0025	0.0406	0.1131	0.0159	0.1142	43.8223	8.0252	7.1067
13	3.4074	-0.2968	0.018	2.5493	0.8419	3.5893	-0.0361	-0.3879	0.0658	0.1761	0.0511	0.1997	-0.0965	-0.1597	-0.0001	0.1022	-0.0076	0.0367	0.1398	0.0089	0.1005	36.8104	15.3565	20.5399
14	3.8097	5.0012	-5.176	7.6424	-5.8125	7.857	0.2182	-0.0705	-0.7747	-0.0938	-0.2083	-0.5392	0.4351	0.4582	0.0848	0.1434	0.0352	-0.0337	0.1208	-0.0277	0.2362	28.7605	4.6431	48.7551
15	5.8438	1.4446	-1.5991	2.4544	-1.6024	6.1317	0.0391	-0.0987	0.1602	0.267	-0.0879	-0.2717	-0.442	0.5707	0.0334	0.1663	-0.0106	-0.035	0.1372	-0.0126	0.1628	31.0295	19.4404	47.1391
16	6.0188	-1.5643	-2.7245	4.2259	2.2108	3.8859	-0.2411	0.6724	-0.2122	-0.4797	-0.1353	0.5725	-0.4167	-0.4349	0.2567	0.2229	0.0177	-0.0459	0.2351	-0.0288	0.1468	18.4725	19.0254	31.8349
17	4.1801	-1.8581	-1.6439	7.4142	1.6062	6.3472	0.0642	0.2319	-0.0956	0.1476	0.1045	0.5024	0.1521	-0.1018	0.2454	0.1729	0.0601	-0.0434	0.1745	-0.0036	0.1419	15.1167	24.966	42.8009
18	2.6841	-0.7177	-1.1374	2.302	0.7173	3.9003	-0.0803	0.0561	0.0242	0.2081	-0.116	0.0011	-0.3087	-0.2201	0.0733	0.1023	0.0073	-0.0211	0.0815	-0.0059	0.1145	24.1354	20.8359	41.9556
19	4.3068	-5.181	-1.9608	7.1085	1.0764	2.8944	0.5785	0.3369	0.8624	-0.6496	-0.0878	-0.4693	-0.7338	0.2379	-0.347	0.2044	0.0187	0.0607	0.213	0.0327	0.1895	27.4507	28.7653	30.8101
20	4.838	-1.7471	-0.7138	5.9574	0.7767	5.7215	-0.0913	-0.0162	0.339	-0.0285	0.0791	-0.3229	-0.105	0.0469	-0.0226	0.085	-0.0508	0.0133	0.0986	0.0205	0.123	27.0696	24.0047	37.7045
21	3.6002	-0.3946	-0.4059	3.497	-0.3461	3.8273	-0.0733	0.249	-0.3219	-0.1385	0.055	-0.047	0.2837	-0.1872	-0.0347	0.117	-0.0257	-0.0205	0.0976	-0.0315	0.1472	23.2562	9.2428	43.6966
22	6.3182	-3.6866	3.9946	6.8728	-4.7619	3.8668	-0.0989	-0.6205	-0.5584	0.3725	0.29	0.5752	0.1431	-0.7531	-0.2979	0.214	-0.0315	0.0785	0.2491	0.0277	0.2328	13.7185	14.4532	52.9997
23	3.2881	0.8129	0.5249	3.7535	0.949	2.1991	-0.0432	-0.0091	-0.063	0.2311	0.0551	-0.5034	0.3146	0.4867	-0.0621	0.125	0.0552	-0.01	0.1721	-0.0074	0.1673	16.335	-16.3341	45.7449
24	3.001	1.1335	-0.9708	3.0795	-0.1271	2.7439	-0.0231	-0.1222	0.2266	0.1487	0.0391	0.1218	-0.069	0.1206	-0.0077	0.1258	0.0187	-0.0192	0.1138	0.0026	0.1315	9.0688	-7.0022	51.421
25	6.0508	-0.9021	-0.9687	4.9273	0.6728	5.0574	-0.1238	0.418	-0.0844	-0.2209	-0.0368	0.4258	0.3638	-0.2721	0.1235	0.1481	-0.0078	-0.0352	0.1582	-0.0177	0.1225	3.8634	-19.1627	41.5769

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 43 THROUGH 52 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 53 THROUGH 67 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 68 THROUGH 76 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 77 THROUGH 141 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 142 THROUGH 173 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 174 THROUGH 185 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 43 THROUGH 67 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 68 THROUGH 76 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 77 THROUGH 95 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 96 THROUGH 117 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 118 THROUGH 127 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 128 THROUGH 141 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 142 THROUGH 185 )
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESID 43 THROUGH 52 )
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESID 53 THROUGH 76 )
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESID 77 THROUGH 87 )
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESID 88 THROUGH 95 )
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESID 96 THROUGH 117 )
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESID 118 THROUGH 127 )
20	X-RAY DIFFRACTION	20	CHAIN C AND (RESID 128 THROUGH 141 )
21	X-RAY DIFFRACTION	21	CHAIN C AND (RESID 142 THROUGH 173 )
22	X-RAY DIFFRACTION	22	CHAIN C AND (RESID 174 THROUGH 185 )
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESID 43 THROUGH 76 )
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESID 77 THROUGH 153 )
25	X-RAY DIFFRACTION	25	CHAIN D AND (RESID 154 THROUGH 185 )

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