PDB-6qjc: Dimethyl disulfide inhibited sulfur oxygenase reductase

ID or keywords:

Entry

Database: PDB / ID: 6qjc

Title

Dimethyl disulfide inhibited sulfur oxygenase reductase

Components

Sulfur oxygenase/reductase

Keywords

OXIDOREDUCTASE / SULFUR OXYGENASE REDUCTASE / 2-HIS-1-CARBOXYLATE FACIAL TRIAD / CYSTEINE PERSULPHUrATION / BIOGEOCHEMICAL SULFUR CYCLE

Function / homology

sulfur oxygenase/reductase /

sulfur oxygenase/reductase activity / Sulphur oxygenase reductase / Sulphur oxygenase reductase / Dimeric alpha-beta barrel /

metal ion binding /

cytoplasm /

: /

Sulfur oxygenase/reductase

Function and homology information

Biological species

Acidianus ambivalens (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Frazao, C. / Klezin, A. / Poell, U.

Funding support

Portugal,

Germany, 2items

Citation

Journal: To Be Published
Title: Multiple sulfane modifications in active-site cysteine thiols of two sulfur oxygenase reductases and analysis of substrate/product channels
Authors: Frazao, C. / Klezin, A.

History

Deposition	Jan 24, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 5, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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	6qjc.cif.gz	513.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6qjc.ent.gz	429.8 KB	Display	PDB format
PDBx/mmJSON format	6qjc.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/qj/6qjc ftp://data.pdbj.org/pub/pdb/validation_reports/qj/6qjc	HTTPS FTP

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Related structure data

Related structure data	6qkaC 6qkmC 6qmvC 6qneC 6qo0C 6qpaC 2cb2S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2yaw-1 6qmv-1 2yav-1 6qne-1 2yax-1 6qkm-1 3bxv-1 6m35-1 6m3x-d 2cb2-1 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

Deposited unit

A: Sulfur oxygenase/reductase

B: Sulfur oxygenase/reductase

C: Sulfur oxygenase/reductase

D: Sulfur oxygenase/reductase

hetero molecules

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

1

A: Sulfur oxygenase/reductase

B: Sulfur oxygenase/reductase

C: Sulfur oxygenase/reductase

D: Sulfur oxygenase/reductase

hetero molecules

x 6

defined by author&software
Evidence: microscopy, Spheric assembly of 24 monomers with 432 point group symmetry
853 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_785	-y+2,x-y+3,z	1
crystal symmetry operation	3_475	-x+y-1,-x+2,z	1
crystal symmetry operation	10_777	-y+2,-x+2,-z+5/2	1
crystal symmetry operation	11_457	-x+y-1,y,-z+5/2	1
crystal symmetry operation	12_587	x,x-y+3,-z+5/2	1

Unit cell

Length a, b, c (Å)	158.400, 158.400, 227.960
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	182
Space group name H-M	P6₃22

Components on special symmetry positions

ID	Model	Components
1	1	D-752- HOH

#1: Protein	Sulfur oxygenase/reductase / / Sulfur oxygenase reductase / SOR Mass: 35484.074 Da / Num. of mol.: 4 / Mutation: Cys31Tsy, Cys101Css, Cys104Css Source method: isolated from a genetically manipulated source Details: RESIDUES CYS_31 APPEAR DERIVATIZED INTO TSY_31, RESIDUES CYS_101 APEAR DERIVATIZED INTO CSS_101 AND RESIDUES CYS_104 APPPEAR DERIVATIZED INTO CSS_104, BY CHEMICAL MODIFICATION Source: (gene. exp.) Acidianus ambivalens (archaea) / Gene: sor / Production host: Escherichia coli (E. coli) / References: UniProt: P29082, sulfur oxygenase/reductase
#2: Chemical	ChemComp-FE / FE (III) ION / Iron Mass: 55.845 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 919 / 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: 2.93 Å³/Da / Density % sol: 57.97 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 0.1 M sodium cacodylate, pH 6.1; 1.4 M sodium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 7, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.7→111.5 Å / Num. obs: 183638 / % possible obs: 99.9 % / Redundancy: 14.4 % / B_iso Wilson estimate: 30 Å² / CC_1/2: 0.99 / R_pim(I) all: 0.03 / R_rim(I) all: 0.35 / R_sym value: 0.35 / Net I/σ(I): 20.7
Reflection shell	Resolution: 1.7→1.74 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS	VERSION March 1, 2015	data reduction
XDS	VERSION March 1, 2015	data scaling
PHASER	2.5.6	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2cb2

2cb2

Resolution: 1.7→79.2 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.21

	R_factor	Num. reflection	% reflection
R_free	0.1877	3230	1.76 %
R_work	0.1645	-	-
obs	0.165	183402	99.86 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.7→79.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9880	0	4	919	10803

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	10412
X-RAY DIFFRACTION	f_angle_d	1.064	14065
X-RAY DIFFRACTION	f_dihedral_angle_d	14.985	3963
X-RAY DIFFRACTION	f_chiral_restr	0.044	1454
X-RAY DIFFRACTION	f_plane_restr	0.005	1815

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 (%)
1.7-1.7254	0.3345	143	0.3061	7716	X-RAY DIFFRACTION	100
1.7254-1.7524	0.2728	133	0.2663	7693	X-RAY DIFFRACTION	100
1.7524-1.7811	0.2733	154	0.2462	7713	X-RAY DIFFRACTION	100
1.7811-1.8118	0.2563	151	0.2309	7683	X-RAY DIFFRACTION	100
1.8118-1.8448	0.2428	131	0.2187	7741	X-RAY DIFFRACTION	100
1.8448-1.8803	0.23	117	0.2027	7760	X-RAY DIFFRACTION	100
1.8803-1.9187	0.2505	133	0.2043	7749	X-RAY DIFFRACTION	100
1.9187-1.9604	0.2357	155	0.1974	7742	X-RAY DIFFRACTION	100
1.9604-2.006	0.2124	133	0.1795	7762	X-RAY DIFFRACTION	100
2.006-2.0562	0.2079	139	0.1677	7789	X-RAY DIFFRACTION	100
2.0562-2.1118	0.1956	140	0.1644	7771	X-RAY DIFFRACTION	100
2.1118-2.1739	0.1775	139	0.1596	7787	X-RAY DIFFRACTION	100
2.1739-2.2441	0.1868	140	0.16	7784	X-RAY DIFFRACTION	100
2.2441-2.3243	0.2003	139	0.156	7808	X-RAY DIFFRACTION	100
2.3243-2.4173	0.1756	140	0.1559	7808	X-RAY DIFFRACTION	100
2.4173-2.5274	0.2047	141	0.158	7840	X-RAY DIFFRACTION	100
2.5274-2.6606	0.1853	140	0.1626	7844	X-RAY DIFFRACTION	100
2.6606-2.8273	0.208	142	0.1564	7892	X-RAY DIFFRACTION	100
2.8273-3.0456	0.1767	141	0.1606	7887	X-RAY DIFFRACTION	100
3.0456-3.3521	0.1657	141	0.156	7920	X-RAY DIFFRACTION	100
3.3521-3.8372	0.1634	143	0.1429	7972	X-RAY DIFFRACTION	100
3.8372-4.8344	0.1453	145	0.1271	8068	X-RAY DIFFRACTION	100
4.8344-79.286	0.1657	150	0.1647	8443	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	0.0813	0.0932	0.0108	0.0606	0.0617	0.2106	0.1278	0.1114	-0.0356	-0.0865	-0.079	0.0052	-0.1286	-0.1328	0.0022	0.2512	0.0037	0.0388	0.1174	0.0115	0.1674	-79.2809	181.3555	270.8508
2	0.0257	0.0186	-0.0072	0.0113	-0.004	0.0013	-0.1057	0.0956	-0.0658	-0.0014	0.0911	0.0832	-0.0957	-0.0409	0	0.2537	-0.0013	0.0132	0.1673	-0.0289	0.2326	-80.4982	187.1819	277.8559
3	0.0119	0.0729	-0.0429	0.0935	-0.1352	0.2114	-0.0035	0.1036	-0.0359	0.0101	-0.0163	0.0261	0.1273	0.0979	0	0.2549	0.0231	0.0186	0.1764	-0.0244	0.1855	-76.4245	173.9744	265.2844
4	0.0045	0.0027	-0.001	0.0095	0.0002	0.0079	-0.027	0.115	-0.0844	0.0096	0.0943	-0.0839	0.1655	0.0453	-0	0.4037	-0.046	-0.0016	0.2177	-0.1151	0.3105	-100.3657	172.6873	246.9086
5	0.1237	0.0357	0.1006	0.0211	0.1172	0.3481	0.0273	0.0673	-0.0488	-0.0025	-0.0207	0.0044	0.1453	-0.0057	-0.0022	0.2262	-0.0142	0.0198	0.0993	0.0017	0.1811	-83.6167	171.1393	273.6514
6	0.0678	-0.0815	0.0435	0.1132	0.0307	0.127	0.0158	0.0917	-0.0537	0.0235	-0.0059	-0.0109	0.1205	-0.0876	0.0027	0.2394	-0.0512	0.0141	0.1484	-0.0025	0.1827	-93.5206	172.6913	272.2872
7	0.0337	0.049	-0.0496	0.3707	-0.2151	0.1745	-0.0672	-0.2907	-0.0535	-0.1095	0.0682	0.0349	-0.0565	-0.3179	0.0767	0.1094	0.0885	-0.0024	0.2449	-0.0787	0.1332	-77.5335	207.3721	240.6402
8	0.0488	-0.0022	0.0135	0.1317	0.0775	0.0623	-0.0234	-0.0459	0.0336	-0.0631	-0.0014	-0.0442	0.1207	-0.057	0	0.126	0.0136	0.0096	0.1633	-0.0116	0.1542	-79.6235	203.7799	242.3685
9	0.0016	0.0052	-0.0029	0.0094	-0.0071	0.0045	0.0685	-0.1357	0.0292	-0.0286	0.0406	0.1139	0.0222	0.0164	-0.0007	0.1747	0.0184	0.005	0.2131	-0.0407	0.187	-74.4842	206.7236	250.131
10	0.1811	-0.0999	-0.061	0.061	0.0557	0.0503	-0.0129	0.0747	0.0739	-0.0604	0.0223	0.0073	0.045	-0.0162	0	0.1477	-0.0031	0.0009	0.1784	-0.0018	0.1625	-78.8738	205.3409	231.2309
11	0.2396	0.1564	-0.2393	0.1042	-0.1571	0.2417	-0.0516	0.3865	0.0833	-0.0632	0.2152	0.0192	0.0637	-0.0762	0.0648	0.2411	-0.0803	-0.0221	0.2621	-0.0515	0.1948	-102.987	185.986	239.9898
12	0.1896	0.0124	0.044	0.0003	0.065	0.1736	-0.0218	0.0391	-0.0058	-0.0325	0.0264	0.0007	0.0717	-0.0299	0	0.1277	0.0141	0.0147	0.1119	-0.0139	0.1326	-74.2927	196.0329	236.6677
13	0.0749	0.0014	0.0219	0.0246	-0.0025	0.1783	0.0049	0.0031	-0.0169	-0.0591	0.0105	0.0437	0.1061	-0.0316	0	0.1633	0.0071	0.0128	0.1397	-0.0135	0.1666	-77.3746	188.2869	241.6621
14	0.1171	-0.076	-0.0421	0.0468	0.0157	0.2039	0.0742	-0.0655	0.0047	-0.1189	-0.1522	-0.1905	0.1809	-0.2017	-0.0413	0.1376	-0.0764	-0.0004	0.1372	0.0246	0.2431	-113.0508	192.9804	283.5781
15	0.0541	-0.0139	-0.0374	0.0931	0.0597	0.0823	-0.0263	-0.0208	0.0166	-0.1045	0.0297	-0.1122	0.1193	-0.1217	0	0.18	-0.0523	0.0025	0.1982	0.0003	0.1994	-113.7493	193.3605	278.4457
16	0.0073	-0.0005	-0.0063	0.0006	-0.0026	0.0116	0.0367	0.1143	0.0457	0.0281	0.1241	0.0151	0.149	0.0277	0.0001	0.183	-0.0645	0.0005	0.2122	-0.0246	0.2088	-111.5886	202.5798	281.0442
17	0.262	-0.1487	0.1089	0.0899	-0.0147	0.0532	-0.0382	-0.0362	-0.0339	0.0399	0.0013	0.0468	0.1598	-0.0367	-0.0001	0.2335	-0.0792	0.0301	0.1946	-0.0039	0.185	-118.0884	184.7804	283.5979
18	0.0572	-0.0453	-0.1077	0.0986	0.1718	0.324	-0.0598	-0.1022	-0.1738	0.0648	0.0158	0.1411	0.3057	-0.0344	-0.0104	0.289	-0.1158	0.0062	0.2144	-0.0274	0.2672	-110.1021	177.746	253.7213
19	0.1671	-0.0498	0.0058	0.1491	0.0775	0.2894	-0.0718	-0.0162	-0.0348	-0.016	-0.0339	0.039	0.4034	-0.0604	-0.1273	0.0829	-0.1603	-0.0102	0.191	-0.0223	0.1497	-125.2334	190.336	280.0453
20	0.0859	-0.022	0.03	0.168	0.0903	0.122	0.0068	-0.0336	-0.0103	-0.0783	-0.0088	0.009	0.073	-0.0655	-0.0197	0.1314	-0.0601	0.0022	0.1939	-0.0037	0.1403	-122.8383	195.8011	266.6678
21	0.0243	0.0024	-0.008	0.5305	0.1028	0.0998	0.041	-0.2407	-0.2134	-0.0222	-0.2153	-0.1336	0.0268	-0.0765	-0.1261	0.1067	-0.0964	-0.0672	0.2995	0.0543	0.1435	-115.3117	219.3382	254.108
22	0.0672	-0.0913	0.046	0.1184	-0.0669	0.0585	0.0679	-0.0143	-0.0841	0.0439	-0.0676	-0.0366	-0.0424	-0.0418	0	0.1446	-0.03	-0.0084	0.2081	-0.0121	0.139	-111.5933	215.5764	249.4774
23	0.012	-0.0138	-0.0127	0.0117	0.0126	0.0131	0.0236	0.1017	-0.024	0.0962	-0.0502	0.0324	0.0659	0.06	-0.0031	0.1763	-0.0365	-0.0503	0.2078	-0.0007	0.1641	-105.578	222.1416	253.2129
24	-0.0043	0.0152	0.007	0.1036	-0.1839	0.2728	-0.0165	-0.0053	0.0291	0.0467	0.0041	0.0408	-0.0097	-0.1044	0.0001	0.1362	-0.0381	-0.0236	0.2056	-0.0116	0.1879	-123.2329	217.3711	248.0102
25	0.1019	-0.1281	0.0266	0.1596	-0.0321	0.008	-0.1181	0.1308	-0.0331	-0.1004	0.1284	0.3244	-0.0116	-0.0277	-0.0025	0.2442	-0.0983	-0.035	0.228	-0.0351	0.2306	-113.3983	186.7198	246.1791
26	0.0594	0.0765	0.0338	0.1565	-0.0277	0.1494	-0.0205	-0.0038	-0.0352	0.0089	0.0001	0.029	0.0114	-0.0417	-0.0625	0.0472	-0.0336	-0.018	0.1221	-0.01	0.0808	-114.5748	216.5986	240.0105
27	0.1049	0.0042	0.1073	0.0894	-0.0776	0.1461	-0.0194	0.0385	-0.0389	-0.0146	-0.0106	-0.0205	0.0343	-0.0855	0	0.1428	-0.0364	-0.0149	0.1663	-0.0043	0.1475	-107.8083	210.0831	237.1712

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:66)
2	X-RAY DIFFRACTION	2	(chain A and resid 67:76)
3	X-RAY DIFFRACTION	3	(chain A and resid 77:137)
4	X-RAY DIFFRACTION	4	(chain A and resid 138:149)
5	X-RAY DIFFRACTION	5	(chain A and resid 150:268)
6	X-RAY DIFFRACTION	6	(chain A and resid 269:308)
7	X-RAY DIFFRACTION	7	(chain B and resid 2:21)
8	X-RAY DIFFRACTION	8	(chain B and resid 22:65)
9	X-RAY DIFFRACTION	9	(chain B and resid 66:76)
10	X-RAY DIFFRACTION	10	(chain B and resid 77:129)
11	X-RAY DIFFRACTION	11	(chain B and resid 130:148)
12	X-RAY DIFFRACTION	12	(chain B and resid 149:269)
13	X-RAY DIFFRACTION	13	(chain B and resid 270:308)
14	X-RAY DIFFRACTION	14	(chain C and resid 2:22)
15	X-RAY DIFFRACTION	15	(chain C and resid 23:65)
16	X-RAY DIFFRACTION	16	(chain C and resid 66:76)
17	X-RAY DIFFRACTION	17	(chain C and resid 77:130)
18	X-RAY DIFFRACTION	18	(chain C and resid 131:150)
19	X-RAY DIFFRACTION	19	(chain C and resid 151:246)
20	X-RAY DIFFRACTION	20	(chain C and resid 247:308)
21	X-RAY DIFFRACTION	21	(chain D and resid 2:26)
22	X-RAY DIFFRACTION	22	(chain D and resid 27:66)
23	X-RAY DIFFRACTION	23	(chain D and resid 67:76)
24	X-RAY DIFFRACTION	24	(chain D and resid 77:129)
25	X-RAY DIFFRACTION	25	(chain D and resid 130:148)
26	X-RAY DIFFRACTION	26	(chain D and resid 149:268)
27	X-RAY DIFFRACTION	27	(chain D and resid 269:308)

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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+About Yorodumi

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-Aug 12, 2020. Covid-19 info

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Download

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Validation report

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi