PDB-8t4c: Membrane-associated thioredoxin oxidoreductase FetE from Campylob...

ID or keywords:

Entry

Database: PDB / ID: 8t4c

Title

Membrane-associated thioredoxin oxidoreductase FetE from Campylobacter jejuni

Components

Thioredoxin oxidoreductase

Keywords

OXIDOREDUCTASE / Fet system / iron uptake / disulfide reductase

Function / homology

Function and homology information

antioxidant activity / oxidoreductase activity
Similarity search - Function

Biological species

Campylobacter jejuni subsp. jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Chan, A.C. / Murphy, M.E.

Funding support

Canada, 2items

Citation

Journal: Biorxiv / Year: 2023
Title: Dissecting components of the Campylobacter jejuni fetMP-fetABCDEF gene cluster in iron scavenging.
Authors: Richardson-Sanchez, T. / Chan, A.C.K. / Sabatino, B. / Lin, H. / Gaynor, E.C. / Murphy, M.E.P.

History

Deposition	Jun 9, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 9, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8t4c.cif.gz	179.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8t4c.ent.gz	144.4 KB	Display	PDB format
PDBx/mmJSON format	8t4c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8t4c_validation.pdf.gz	448.3 KB	Display	wwPDB validaton report
Full document	8t4c_full_validation.pdf.gz	448.7 KB	Display
Data in XML	8t4c_validation.xml.gz	15.1 KB	Display
Data in CIF	8t4c_validation.cif.gz	21.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t4/8t4c ftp://data.pdbj.org/pub/pdb/validation_reports/t4/8t4c	HTTPS FTP

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Related structure data

Similar structure data	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	#233 - May 2019 S-Nitrosylated Hemoglobin similarity (2) #91 - Jul 2007 Thymine Dimers similarity (2)

Deposited unit

A: Thioredoxin oxidoreductase

B: Thioredoxin oxidoreductase

hetero molecules

32.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Thioredoxin oxidoreductase

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

2

B: Thioredoxin oxidoreductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.250, 43.380, 71.860
Angle α, β, γ (deg.)	90.00, 108.41, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Thioredoxin oxidoreductase Mass: 16357.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter) Strain: 81-176 / Gene: CJJ81176_1655, FetE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3PAZ9
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.75 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: 1.8 M ammonium sulfate, 0.1 M sodium acetate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.97949 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 20, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection

Resolution: 1.5→50 Å / Num. obs: 46005 / % possible obs: 99.2 % / Redundancy: 4.2 % / CC_1/2: 0.999 / R_merge(I) obs: 0.048 / R_rim(I) all: 0.052 / Net I/σ(I): 16.69

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.5-1.6	0.215	7863	0.935	0.267	1
1.6-1.71	0.147	6811	0.977	0.175	1
1.71-1.84	0.091	6114	0.99	0.109	1
1.84-2	0.071	5532	0.995	0.082	1
2-2.18	0.068	4430	0.996	0.077	1
2.18-2.41	0.072	3923	0.994	0.081	1
2.41-2.68	0.074	3053	0.995	0.081	1
2.68-3.03	0.06	2517	0.997	0.065	1
3.03-3.49	0.047	1963	0.998	0.051	1
3.49-4.11	0.037	1449	0.999	0.04	1
4.11-5	0.034	1026	0.999	0.037	1
5-50	0.035	1324	0.999	0.038	1

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XSCALE		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→46.73 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 17.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1832	4316	4.99 %
R_work	0.1558	-	-
obs	0.1572	43746	95.75 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.5→46.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2225	0	11	270	2506

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2277
X-RAY DIFFRACTION	f_angle_d	1.081	3073
X-RAY DIFFRACTION	f_dihedral_angle_d	5.85	294
X-RAY DIFFRACTION	f_chiral_restr	0.083	362
X-RAY DIFFRACTION	f_plane_restr	0.007	387

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 (%)
1.5-1.52	0.2525	115	0.2543	2146	X-RAY DIFFRACTION	76
1.52-1.53	0.2836	123	0.2423	2285	X-RAY DIFFRACTION	80
1.53-1.55	0.2554	138	0.2221	2607	X-RAY DIFFRACTION	90
1.55-1.57	0.259	142	0.2107	2665	X-RAY DIFFRACTION	94
1.57-1.59	0.2225	145	0.192	2722	X-RAY DIFFRACTION	96
1.59-1.62	0.2215	142	0.1731	2776	X-RAY DIFFRACTION	96
1.62-1.64	0.2125	149	0.1703	2777	X-RAY DIFFRACTION	96
1.64-1.66	0.2045	140	0.1763	2748	X-RAY DIFFRACTION	96
1.66-1.69	0.1784	142	0.1811	2740	X-RAY DIFFRACTION	96
1.69-1.72	0.232	148	0.1722	2761	X-RAY DIFFRACTION	96
1.72-1.75	0.2143	140	0.1754	2718	X-RAY DIFFRACTION	95
1.75-1.78	0.2104	146	0.1785	2742	X-RAY DIFFRACTION	96
1.78-1.81	0.2136	150	0.187	2782	X-RAY DIFFRACTION	96
1.81-1.85	0.1953	142	0.1793	2700	X-RAY DIFFRACTION	97
1.85-1.89	0.214	146	0.1615	2822	X-RAY DIFFRACTION	96
1.89-1.93	0.1794	147	0.1603	2730	X-RAY DIFFRACTION	96
1.93-1.98	0.1637	147	0.143	2770	X-RAY DIFFRACTION	97
1.98-2.04	0.1847	148	0.1491	2741	X-RAY DIFFRACTION	96
2.04-2.1	0.1713	135	0.1539	2703	X-RAY DIFFRACTION	95
2.1-2.16	0.1734	144	0.1574	2830	X-RAY DIFFRACTION	98
2.16-2.24	0.1551	149	0.15	2799	X-RAY DIFFRACTION	98
2.24-2.33	0.1898	145	0.1412	2805	X-RAY DIFFRACTION	99
2.33-2.44	0.2215	145	0.1473	2883	X-RAY DIFFRACTION	99
2.44-2.56	0.1834	150	0.1454	2837	X-RAY DIFFRACTION	99
2.56-2.72	0.2215	152	0.1574	2830	X-RAY DIFFRACTION	99
2.73-2.94	0.1907	152	0.1573	2864	X-RAY DIFFRACTION	100
2.94-3.23	0.1648	150	0.1528	2839	X-RAY DIFFRACTION	100
3.23-3.7	0.1648	148	0.143	2865	X-RAY DIFFRACTION	100
3.7-4.66	0.1437	147	0.1248	2857	X-RAY DIFFRACTION	100
4.66-46.73	0.1952	149	0.1792	2857	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	2.0459	-0.6149	0.5911	0.4204	-0.6974	1.9755	-0.1686	-0.3861	-0.1721	0.3122	-0.0859	0.8139	0.3184	-0.4394	0.1601	0.4475	-0.0752	0.0871	0.3209	-0.0477	0.4036	11.2647	5.5202	-0.055
2	2.9734	-2.0833	-1.8213	3.9507	2.2656	3.6692	-0.1771	-0.1368	-0.2182	0.2273	0.0332	0.47	0.3941	-0.3416	0.13	0.2924	-0.0441	0.016	0.3007	0.0257	0.2065	9.8016	10.669	0.8974
3	1.2885	0.3118	-0.0403	1.5481	0.7413	2.3153	-0.1365	0.0835	0.0388	-0.0116	-0.1023	0.3621	-0.115	-0.691	0.1888	0.214	0.021	-0.0029	0.3715	-0.0334	0.2288	7.5274	19.5293	-1.1834
4	3.2677	0.671	1.983	0.9339	1.0021	3.5509	-0.0947	0.0915	0.1979	-0.1354	0.0401	-0.0926	-0.3114	-0.1336	0.0799	0.2966	0.0024	0.0037	0.2215	0.0092	0.197	17.983	26.8172	-8.1639
5	1.1253	0.0135	0.0089	1.8325	-0.1449	3.1243	0.1106	0.159	-0.0253	-0.0346	0.0051	0.2644	0.0955	-0.3487	-0.1428	0.218	0.0206	-0.0203	0.3312	0.0011	0.2178	8.9839	21.2775	-8.0807
6	2.0502	-0.946	-0.2808	2.0663	0.3254	0.525	-0.0425	-0.3096	0.214	0.1939	0.1165	0.0782	-0.1977	-0.1697	-0.046	0.2708	0.0318	-0.02	0.2518	-0.0395	0.2111	16.9543	30.2177	6.0471
7	1.2619	-0.1405	-0.4169	1.6692	0.3371	1.2676	-0.132	-0.0788	-0.0328	0.1306	0.0611	0.0852	-0.0309	-0.2233	0.0936	0.2414	0.0141	-0.0013	0.2574	-0.0102	0.157	15.351	18.9565	2.568
8	2.1453	-0.3865	0.2485	1.1719	-0.2594	2.0641	-0.1394	0.2718	-0.122	-0.162	0.1388	0.0368	0.2569	0.0638	-0.0212	0.2777	-0.0356	-0.0039	0.2468	-0.0135	0.1602	18.069	12.7403	-8.7361
9	4.8561	1.422	1.5262	3.2048	0.9132	3.2633	-0.1815	0.1756	-0.0154	-0.4453	0.084	-0.0071	-0.0621	0.0645	0.0556	0.2705	0.0025	-0.0011	0.2848	0.0066	0.1545	17.6618	18.2475	-17.0421
10	2.6966	0.187	-0.7698	1.5055	-0.1865	1.5856	-0.0075	0.1567	0.0928	-0.1832	-0.0261	-0.0308	-0.0223	0.0161	0.0555	0.1988	0.0151	-0.0069	0.1566	0.0077	0.1672	-0.7454	17.7489	26.9567
11	2.3437	-0.8287	-0.0406	3.7332	-4.0045	4.8343	-0.0424	-0.0545	0.4774	0.1804	0.0313	-0.0688	-0.3479	0.011	-0.0454	0.1644	-0.0061	-0.0075	0.1493	-0.0238	0.2766	3.1474	30.9772	33.0002
12	1.5754	0.1537	-0.3759	1.939	-0.191	0.6521	-0.0332	0.0998	0.0325	-0.1756	0.0186	-0.1287	0.0283	-0.022	0.0065	0.1434	0.0007	-0.0061	0.1467	0.001	0.168	2.0554	19.9953	30.979

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 28 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 60 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 61 through 80 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 81 through 91 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 92 through 106 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 107 through 131 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 132 through 150 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 151 through 162 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 23 through 69 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 70 through 80 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 81 through 162 )

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