PDB-4nxl: Dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis

ID or keywords:

Entry

Database: PDB / ID: 4nxl

Title

Dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis

Components

DszC

Keywords

OXIDOREDUCTASE / monooxygenase

Function / homology

Function and homology information

oxidoreductase activity, acting on the CH-CH group of donors / flavin adenine dinucleotide binding
Similarity search - Function

Biological species

Rhodococcus erythropolis (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Zhang, L. / Duan, X. / Li, X. / Rao, Z.

Citation

Journal: Proteins / Year: 2014
Title: Structural insights into the stabilization of active, tetrameric DszC by its C-terminus.
Authors: Zhang, L. / Duan, X. / Zhou, D. / Dong, Z. / Ji, K. / Meng, W. / Li, G. / Li, X. / Yang, H. / Ma, T. / Rao, Z.

History

Deposition	Dec 9, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 23, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 8, 2014	Group: Database references
Revision 1.2	Nov 12, 2014	Group: Structure summary
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4nxl.cif.gz	608 KB	Display	PDBx/mmCIF format
PDB format	pdb4nxl.ent.gz	506 KB	Display	PDB format
PDBx/mmJSON format	4nxl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4nxl_validation.pdf.gz	467.1 KB	Display	wwPDB validaton report
Full document	4nxl_full_validation.pdf.gz	480.6 KB	Display
Data in XML	4nxl_validation.xml.gz	60 KB	Display
Data in CIF	4nxl_validation.cif.gz	85.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nx/4nxl ftp://data.pdbj.org/pub/pdb/validation_reports/nx/4nxl	HTTPS FTP

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Related structure data

Similar structure data	4jek-1 3x0x-2 3x0y-2 3x0y-1 4jek-2 3x0x-1 5xdc-d 5xde-d 5xdb-d 5xdg-d 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: DszC

B: DszC

C: DszC

D: DszC

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	130.980, 136.180, 174.830
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	C-641- HOH

#1: Protein	DszC Mass: 48904.117 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Strain: DS-3 / Gene: dszC / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q64F43
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 622 / 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: 1.99 Å³/Da / Density % sol: 38.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 200 mM lithium sulfate, 100 mM bis-tris [pH 6.5] and 35% [w/v] PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 1, 2013

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.26→50 Å / Num. obs: 69343 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.26-2.32	2.14	0.985	1.37	1	97.6
2.32-2.38	2.16	0.564	2.05	1	99.8
2.38-2.45	2.17	0.568	2.12	1	99.5
2.45-2.53	2.17	0.431	2.73	1	99.5
2.53-2.61	2.18	0.402	2.82	1	99.4
10.11-50	2.21	0.027	25.13	1	92.6

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASES		phasing
PHENIX	(phenix.refine: dev_1525)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→36.355 Å / SU ML: 0.27 / σ(F): 1.36 / Phase error: 21.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2313	3509	5.06 %	RANDOM
R_work	0.1794	-	-	-
all	0.19344	69447	-	-
obs	0.1821	69343	99.85 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→36.355 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12164	0	0	622	12786

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	12464
X-RAY DIFFRACTION	f_angle_d	1.193	17000
X-RAY DIFFRACTION	f_dihedral_angle_d	13.638	4372
X-RAY DIFFRACTION	f_chiral_restr	0.051	1852
X-RAY DIFFRACTION	f_plane_restr	0.006	2260

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 (%)
2.3-2.3315	0.2672	132	0.2092	2573	X-RAY DIFFRACTION	100
2.3315-2.3648	0.2645	153	0.208	2654	X-RAY DIFFRACTION	100
2.3648-2.4001	0.3062	120	0.215	2591	X-RAY DIFFRACTION	100
2.4001-2.4376	0.3285	135	0.2265	2608	X-RAY DIFFRACTION	100
2.4376-2.4776	0.2941	115	0.213	2665	X-RAY DIFFRACTION	100
2.4776-2.5203	0.2667	133	0.2071	2609	X-RAY DIFFRACTION	100
2.5203-2.5661	0.2654	138	0.1971	2612	X-RAY DIFFRACTION	100
2.5661-2.6154	0.2643	147	0.1977	2617	X-RAY DIFFRACTION	100
2.6154-2.6688	0.2466	140	0.2048	2588	X-RAY DIFFRACTION	100
2.6688-2.7268	0.2772	135	0.2032	2628	X-RAY DIFFRACTION	100
2.7268-2.7902	0.2633	127	0.1983	2651	X-RAY DIFFRACTION	100
2.7902-2.86	0.2687	162	0.1921	2618	X-RAY DIFFRACTION	100
2.86-2.9373	0.2636	121	0.1929	2599	X-RAY DIFFRACTION	100
2.9373-3.0236	0.2476	157	0.1934	2614	X-RAY DIFFRACTION	100
3.0236-3.1212	0.2323	133	0.1946	2642	X-RAY DIFFRACTION	100
3.1212-3.2327	0.226	145	0.1888	2609	X-RAY DIFFRACTION	100
3.2327-3.362	0.2556	146	0.1801	2667	X-RAY DIFFRACTION	100
3.362-3.5149	0.2413	132	0.18	2623	X-RAY DIFFRACTION	100
3.5149-3.7001	0.2119	154	0.1763	2602	X-RAY DIFFRACTION	99
3.7001-3.9316	0.2088	136	0.1777	2642	X-RAY DIFFRACTION	99
3.9316-4.2348	0.1733	157	0.1442	2640	X-RAY DIFFRACTION	100
4.2348-4.6601	0.198	143	0.1569	2615	X-RAY DIFFRACTION	99
4.6601-5.3327	0.1963	154	0.1527	2672	X-RAY DIFFRACTION	100
5.3327-6.7117	0.225	144	0.1778	2710	X-RAY DIFFRACTION	100
6.7117-36.3592	0.2072	150	0.1461	2785	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	0.0791	0.0992	-0.0529	0.0899	-0.0102	0.1017	-0.1142	-0.1255	-0.2573	0.1206	-0.059	0.391	0.0647	-0.1031	-0.003	0.3877	0.0179	-0.0804	0.3656	-0.0756	0.3315	18.1527	193.2736	40.4693
2	0.0699	0.1526	-0.0001	0.6291	-0.4119	0.4104	0.0118	-0.1397	0.1685	-0.1593	-0.0936	-0.1307	-0.1841	0.0441	0.0001	0.3302	-0.0212	-0.0537	0.2783	-0.0671	0.3514	34.3175	199.2797	32.2002
3	0.0946	-0.1063	0.0557	0.1173	-0.0213	0.1275	-0.0677	-0.0003	0.0989	-0.1348	-0.1235	-0.0176	-0.2648	0.0923	0.0007	0.4906	-0.068	-0.0293	0.3562	-0.0074	0.6709	35.6041	214.3146	22.7524
4	0.3768	0.1137	0.119	0.3635	0.1624	0.2817	0.0257	-0.031	0.0648	-0.0213	0.0104	-0.0537	-0.0108	0.0284	-0	0.1872	0.0023	-0.0191	0.2158	-0.0315	0.2455	25.1236	191.8992	23.0777
5	0.4605	-0.4006	-0.0939	0.6013	0.094	0.2583	-0.0695	-0.0025	0.2237	-0.0263	0.0576	-0.0509	0.0811	0.0921	-0.0002	0.2442	0.0218	-0.0063	0.2409	-0.0107	0.3128	-14.6284	197.7566	11.0448
6	0.3041	-0.1222	-0.2436	0.4183	0.2197	0.522	-0.0061	-0.0756	-0.1243	-0.1031	-0.016	-0.0761	0.1196	-0.0361	-0.0002	0.2283	0.0093	-0.0365	0.2647	0.0036	0.2613	-25.8228	189.2149	25.1349
7	0.3693	-0.173	-0.0405	0.2623	0.0664	0.6252	-0.0266	-0.0605	-0.172	-0.0243	0.0765	0.0239	-0.0354	-0.0397	-0.0001	0.239	0.0471	-0.0316	0.2497	0.0352	0.2902	-23.9143	187.3213	28.1615
8	0.4964	0.2821	-0.0638	0.3854	0.0127	0.2266	-0.016	-0.0513	0.0181	-0.033	-0.0231	0.0161	-0.0105	0.0153	-0.0001	0.1903	0.021	-0.0339	0.191	-0.0183	0.2287	-0.5969	185.9869	10.445
9	0.0251	0.0702	0.0343	0.1473	0.063	0.1311	-0.2605	-0.285	-0.0286	-0.0486	0.2789	0.1322	0.4393	-0.1458	-0.001	0.4471	0.0169	-0.1001	0.4091	-0.0347	0.3036	0.49	154.9121	-10.0139
10	0.0902	0.1627	-0.1519	0.1412	-0.1808	0.3734	0.0494	-0.0065	-0.0497	-0.1666	0.1045	0.2181	0.2569	-0.0389	-0.0003	0.3462	0.0099	-0.0986	0.2969	-0.0591	0.2422	0.4686	166.3282	-19.6794
11	0.2743	0.2128	-0.2726	0.1372	-0.1735	0.1621	-0.1229	0.2557	-0.018	-0.3528	0.0956	-0.1261	0.0302	-0.0282	-0.0004	0.5651	0.1033	-0.0159	0.3926	-0.028	0.2813	9.7818	172.1126	-28.9469
12	0.0893	0.0471	0.064	0.0619	0.0822	0.0877	0.0571	0.3024	0.1623	-0.2836	0.2117	0.0886	0.0873	0.0647	0.0004	0.6554	0.1175	0.1041	0.5506	-0.0531	0.3378	19.3233	169.8499	-31.9848
13	0.1603	-0.0935	0.0541	0.5197	-0.3357	0.4117	0.0651	0.0038	0.0013	-0.122	-0.0405	0.0165	0.0659	0.0569	0	0.2334	0.0355	-0.0205	0.1873	-0.004	0.19	9.1355	171.9593	-9.6533
14	0.4434	-0.3414	0.1786	0.4563	0.1767	0.3658	0.0023	-0.063	-0.0285	0.0094	-0.0392	-0.0716	-0.091	0.0188	-0.0002	0.2519	0.0375	-0.0217	0.2629	-0.0018	0.2295	35.286	152.8186	17.3053
15	0.1729	0.2606	-0.0698	0.5064	-0.0028	0.1383	-0.1461	-0.1434	-0.0525	0.1071	0.1421	0.0766	-0.0858	0.015	-0.0067	0.2556	0.1024	-0.0046	0.3036	0.0768	0.3605	23.4899	139.0387	28.587
16	0.0899	-0.1832	-0.1386	0.6631	0.6917	0.6437	0.0506	-0.4866	0.2159	-0.1856	0.1073	0.326	-0.3194	-0.0977	0.0893	0.2682	0.0797	-0.0171	0.4142	0.0745	0.2983	17.633	138.4162	26.4777
17	0.3925	-0.1588	-0.445	0.5634	-0.2092	0.3761	-0.1071	-0.0044	0.0058	0.0227	0.1868	0.1037	-0.0257	0.0139	-0.0002	0.2696	0.0471	-0.0342	0.2737	0.0027	0.2926	21.1808	140.1654	24.1265
18	0.0351	-0.0735	-0.0058	0.3832	0.2534	0.263	-0.0291	0.044	-0.0108	-0.0301	0.0234	-0.2438	0.0449	-0.0488	-0.0007	0.1828	0.043	-0.0037	0.2043	-0.0001	0.2016	27.9084	169.2448	7.301
19	0.6321	-0.1026	0.1196	-0.0568	0.1555	0.3814	0.0188	-0.0821	0.0268	-0.0489	0.0204	0.0091	0.1007	0.0089	0	0.2068	0.0368	-0.033	0.1875	-0.0084	0.1807	21.5328	165.808	18.8867

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 19 through 41 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 42 through 143 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 144 through 169 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 170 through 417 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 19 through 107 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 108 through 169 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 170 through 245 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 246 through 417 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 19 through 41 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 42 through 107 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 108 through 143 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 144 through 169 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 170 through 417 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 19 through 107 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 108 through 159 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 160 through 186 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 187 through 245 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 246 through 295 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 296 through 417 )

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