PDB-8khq: Bifunctional sulfoxide synthase OvoA_Th2 in complex with histidin...

ID or keywords:

Entry

Database: PDB / ID: 8khq

Title

Bifunctional sulfoxide synthase OvoA_Th2 in complex with histidine and cysteine

Components

5-histidylcysteine sulfoxide synthase/putative 4-mercaptohistidine N1-methyltranferase

Keywords

OXIDOREDUCTASE / Metal ion binding / Sulfatase-modifying / Histidine oxygenase / Methyltransferase

Function / homology

Function and homology information

S-adenosylmethionine-dependent methyltransferase activity
Similarity search - Function

Biological species

Hydrogenimonas thermophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.69 Å

Authors

Wang, J. / Ye, K. / Wang, X.Y. / Yan, W.P.

Funding support

China, 1items

Citation

Journal: Acs Catalysis / Year: 2023
Title: Biochemical and Structural Characterization of OvoA Th2 : A Mononuclear Nonheme Iron Enzyme from Hydrogenimonas thermophila for Ovothiol Biosynthesis.
Authors: Wang, X. / Hu, S. / Wang, J. / Zhang, T. / Ye, K. / Wen, A. / Zhu, G. / Vegas, A. / Zhang, L. / Yan, W. / Liu, X. / Liu, P.

History

Deposition	Aug 22, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 6, 2023	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8khq.cif.gz	1.1 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	8khq_validation.pdf.gz	3.6 MB	Display	wwPDB validaton report
Full document	8khq_full_validation.pdf.gz	3.6 MB	Display
Data in XML	8khq_validation.xml.gz	92.6 KB	Display
Data in CIF	8khq_validation.cif.gz	124.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kh/8khq ftp://data.pdbj.org/pub/pdb/validation_reports/kh/8khq	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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #149 - May 2012 Leptin similarity (1) #232 - Apr 2019 Proteins and Biominerals similarity (1) #134 - Feb 2011 Integrin similarity (1) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #69 - Sep 2005 Cholera Toxin similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#228 - Dec 2018
Directed Evolution of Enzymes
similarity (1)
#111 - Mar 2009
Hydrogenase
similarity (1)
#149 - May 2012
Leptin
similarity (1)
#232 - Apr 2019
Proteins and Biominerals
similarity (1)
#134 - Feb 2011
Integrin
similarity (1)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#69 - Sep 2005
Cholera Toxin
similarity (1)
#75 - Mar 2006
Tissue Factor
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)

Deposited unit

A: 5-histidylcysteine sulfoxide synthase/putative 4-mercaptohistidine N1-methyltranferase

B: 5-histidylcysteine sulfoxide synthase/putative 4-mercaptohistidine N1-methyltranferase

C: 5-histidylcysteine sulfoxide synthase/putative 4-mercaptohistidine N1-methyltranferase

D: 5-histidylcysteine sulfoxide synthase/putative 4-mercaptohistidine N1-methyltranferase

hetero molecules

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

1

A: 5-histidylcysteine sulfoxide synthase/putative 4-mercaptohistidine N1-methyltranferase

C: 5-histidylcysteine sulfoxide synthase/putative 4-mercaptohistidine N1-methyltranferase

hetero molecules

defined by author&software
Evidence: gel filtration
171 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 5-histidylcysteine sulfoxide synthase/putative 4-mercaptohistidine N1-methyltranferase

D: 5-histidylcysteine sulfoxide synthase/putative 4-mercaptohistidine N1-methyltranferase

hetero molecules

defined by author&software
171 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.262, 119.114, 412.429
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	5-histidylcysteine sulfoxide synthase/putative 4-mercaptohistidine N1-methyltranferase Mass: 85179.492 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hydrogenimonas thermophila (bacteria) / Gene: SAMN05216234_1259 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1I5R890

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Non-polymers , 5 types, 161 molecules

#2: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-HIS / HISTIDINE Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₀N₃O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CYS / CYSTEINE Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₇NO₂S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.6 Å³/Da / Density % sol: 52.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M BICINE, 17.5% PEG 20000, 3% Dextran sulfate sodium salt

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.97853 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2023

Radiation

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

Radiation wavelength

Wavelength: 0.97853 Å / Relative weight: 1

Reflection

Resolution: 2.69→40 Å / Num. obs: 99655 / % possible obs: 99.7 % / Redundancy: 6.6 % / B_iso Wilson estimate: 58.04 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.096 / R_rim(I) all: 0.104 / Net I/σ(I): 16.46

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.69-2.79	0.828	15738	0.778	0.895	1
2.85-3.05	0.523	14925	0.901	0.567	1
3.05-3.29	0.313	14002	0.962	0.339	1
3.29-3.61	0.176	12886	0.991	0.19	1
3.61-4.03	0.095	11653	0.997	0.103	1
4.03-4.64	0.057	10385	0.999	0.062	1
4.64-5.67	0.045	8901	0.999	0.049	1
5.67-7.93	0.038	7003	0.999	0.041	1
7.93-8.34	0.024	4162	0.999	0.027	1

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Processing

Software

Name	Version	Classification
PHENIX	(1.18.2_3874: ???)	refinement
XDS		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.69→38.7 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2426	4976	5 %
R_work	0.2012	-	-
obs	0.2033	99510	99.62 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.69→38.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23016	0	90	147	23253

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	23768
X-RAY DIFFRACTION	f_angle_d	0.498	32196
X-RAY DIFFRACTION	f_dihedral_angle_d	22.887	8721
X-RAY DIFFRACTION	f_chiral_restr	0.041	3339
X-RAY DIFFRACTION	f_plane_restr	0.003	4125

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 (%)
2.69-2.72	0.3471	159	0.295	3014	X-RAY DIFFRACTION	97
2.72-2.75	0.3655	164	0.296	3124	X-RAY DIFFRACTION	100
2.75-2.79	0.325	165	0.2942	3131	X-RAY DIFFRACTION	100
2.79-2.82	0.3192	162	0.2772	3075	X-RAY DIFFRACTION	100
2.82-2.86	0.3155	164	0.2738	3120	X-RAY DIFFRACTION	100
2.86-2.9	0.3182	166	0.2681	3159	X-RAY DIFFRACTION	100
2.9-2.94	0.3084	161	0.2551	3063	X-RAY DIFFRACTION	100
2.94-2.99	0.3079	166	0.2506	3135	X-RAY DIFFRACTION	100
2.99-3.03	0.2801	165	0.2438	3138	X-RAY DIFFRACTION	100
3.03-3.08	0.2903	163	0.2463	3101	X-RAY DIFFRACTION	100
3.08-3.13	0.279	167	0.2433	3165	X-RAY DIFFRACTION	100
3.13-3.19	0.2778	162	0.2357	3090	X-RAY DIFFRACTION	100
3.19-3.25	0.2531	166	0.2292	3155	X-RAY DIFFRACTION	100
3.25-3.32	0.2834	166	0.2373	3153	X-RAY DIFFRACTION	100
3.32-3.39	0.2649	164	0.2279	3109	X-RAY DIFFRACTION	100
3.39-3.47	0.2645	165	0.2282	3142	X-RAY DIFFRACTION	100
3.47-3.56	0.2498	165	0.218	3126	X-RAY DIFFRACTION	100
3.56-3.65	0.2393	166	0.2124	3145	X-RAY DIFFRACTION	100
3.65-3.76	0.2437	166	0.2012	3169	X-RAY DIFFRACTION	100
3.76-3.88	0.2497	165	0.1981	3125	X-RAY DIFFRACTION	100
3.88-4.02	0.2498	166	0.1866	3165	X-RAY DIFFRACTION	100
4.02-4.18	0.212	165	0.1761	3154	X-RAY DIFFRACTION	100
4.18-4.37	0.1939	167	0.1734	3168	X-RAY DIFFRACTION	100
4.37-4.6	0.203	167	0.1616	3181	X-RAY DIFFRACTION	100
4.6-4.89	0.2079	168	0.1542	3183	X-RAY DIFFRACTION	100
4.89-5.27	0.1783	167	0.1554	3191	X-RAY DIFFRACTION	100
5.27-5.79	0.2195	170	0.1772	3230	X-RAY DIFFRACTION	100
5.79-6.63	0.2408	172	0.1805	3261	X-RAY DIFFRACTION	100
6.63-8.34	0.2279	171	0.183	3251	X-RAY DIFFRACTION	100
8.34-38.7	0.2208	176	0.1891	3311	X-RAY DIFFRACTION	96

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	0.5526	-0.1983	0.0357	1.8873	-0.6024	1.3837	-0.0888	-0.1079	-0.047	-0.0299	0.1553	-0.0533	-0.0474	-0.1264	-0.0799	0.3136	-0.0047	-0.0222	0.5211	0.0904	0.3756	-5.265	-33.564	85.409
2	1.3479	-0.0133	-0.3135	1.4353	0.6195	2.2916	-0.0513	-0.2819	0.2724	0.3163	-0.053	-0.1242	-0.0098	-0.0298	0.1067	0.4772	0.002	-0.0592	0.4497	0.0062	0.4507	-0.731	8.115	66.894
3	0.8487	-0.3136	-0.9155	4.0551	0.8759	2.3293	-0.0318	0.0309	-0.0171	-0.0451	-0.0553	0.0516	0.0361	-0.0597	0.0447	1.0449	0.0227	0.1418	0.6013	-0.0731	1.0867	-6.945	-36.714	69.439
4	1.8834	-0.4619	0.1376	1.1963	-0.1997	1.2536	0.001	-0.2628	-0.4724	0.2666	0.0144	0.1736	0.4079	0.1275	-0.0624	0.7291	0.0042	0.0646	0.4641	0	0.5623	-36.817	-45.721	35.113
5	0.7469	-0.0486	-0.1176	0.9599	-0.1952	1.5368	-0.1072	-0.0843	-0.1922	0.3937	0.0511	0.0601	0.3841	-0.1265	0.0098	0.6914	0.023	0.0538	0.4558	-0.0665	0.5263	-36.359	-39.329	26.747
6	1.2363	0.3633	0.0936	1.034	-0.0958	1.482	-0.0945	-0.003	-0.1864	0.116	0.0472	-0.107	0.1377	0.1733	0.0241	0.4156	0.049	0.0159	0.4816	-0.1163	0.4194	-21.571	-35.895	8.293
7	0.8044	-0.1495	-0.2674	1.2215	1.0609	1.3077	-0.0639	-0.0412	-0.093	0.1466	0.0853	-0.0076	0.0479	-0.0284	0.0099	0.4859	0.0126	0.0035	0.4876	-0.04	0.4462	-36.136	-28.704	21.193
8	0.9733	-0.3047	-0.3408	1.7027	-0.8123	2.0046	0.0367	0.1515	0.0292	-0.8824	-0.0879	0.1128	0.5907	-0.242	0.0888	0.7211	-0.0363	-0.095	0.5887	-0.0544	0.4503	-37.662	1.632	30.157
9	1.0296	0.1515	-0.3182	0.9714	-0.2148	1.83	-0.0549	0.0694	0.4193	-0.1928	-0.0563	-0.1757	-0.4849	0.0036	0.0404	0.5981	0.0393	-0.1085	0.4525	-0.0382	0.499	-34.705	15.608	42.784
10	0.2573	-0.3851	0.1512	0.8992	-0.3979	0.1902	-0.0462	-0.0328	-0.0283	0.0286	-0.0797	0.0349	0.0045	-0.0128	0.0714	0.943	0.139	0.3003	0.6445	-0.096	1.1687	-29.566	-35.097	31.343
11	0.7128	-0.0504	-0.1258	1.0736	-0.4928	0.6074	0.1507	0.7233	1.2549	0.5287	0.204	0.0402	-0.5179	-0.1289	0.2147	0.8547	0.0586	0.0949	0.7599	0.5524	1.3132	-4.265	37.792	27.21
12	0.0444	-0.1071	0.2857	1.1276	-0.6952	1.5872	0.1175	1.0622	1.0004	0.1197	0.2832	0.2835	-0.3734	-0.2434	0.697	0.5787	0.1161	0.069	1.1514	1.052	1.1564	-5.955	34.191	14.416
13	1.4847	-0.151	0.343	1.2069	0.7715	2.1531	-0.0195	0.2846	-0.1009	-0.0631	-0.1105	0.0239	0.1267	-0.0801	0.1285	0.4215	0.0087	0.0765	0.4505	0.0374	0.3809	-0.405	-10.224	33.357
14	0.8831	-0.4154	-0.76	1.928	0.8487	1.1356	-0.0214	-0.0536	-0.1186	-0.0687	0.0088	0.1857	-0.139	-0.1384	-0.0359	0.8886	0.2174	-0.0142	1.0477	0.6769	1.5971	-7.334	32.014	31.464
15	1.026	0.2347	0.4865	2.0614	0.1703	1.6168	-0.0391	0.0165	0.3204	-0.3649	-0.0897	0.3652	-0.407	-0.0197	0.1433	0.5494	0.0041	-0.1494	0.3893	-0.0364	0.523	-36.46	41.319	69.91
16	0.8755	0.2595	0.4029	2.0685	-0.263	1.7227	-0.0245	-0.014	0.1845	-0.4392	-0.0352	0.3423	-0.1267	-0.0129	0.0502	0.4317	0.0046	-0.0439	0.4512	-0.1027	0.53	-35.46	34.978	78.352
17	0.7223	-0.3941	-0.2003	1.0288	-0.078	1.1212	0.0684	-0.0592	0.0551	0.1821	-0.0512	-0.154	-0.1311	0.1813	-0.0079	0.3846	-0.0727	-0.0067	0.6153	-0.1184	0.4148	-20.561	32.101	96.529
18	0.7633	0.458	0.3499	1.2513	0.5089	0.8078	-0.023	-0.0471	0.1061	-0.1054	-0.0378	0.324	-0.0317	-0.0676	0.0553	0.3928	-0.0172	-0.0017	0.5169	-0.0816	0.474	-35.587	24.549	84.182
19	1.2643	0.2948	0.408	1.8342	-1.0763	2.4564	0.0569	-0.1642	-0.2339	0.1054	-0.1291	0.082	0.2447	-0.0375	0.0884	0.4008	-0.0076	-0.0026	0.4419	0.0073	0.3845	-36.282	-13.683	68.661
20	0.2964	0.2597	-0.0702	0.4279	-0.2601	0.2138	0.0027	-0.0107	-0.008	-0.0005	-0.0181	-0.0017	0.0021	0.0056	-0.0126	0.726	-0.0573	-0.3689	0.6067	-0.1905	0.7114	-29.45	30.74	73.663
21	0.878	-0.1904	0.1158	1.8273	-0.3659	1.9668	0.1079	0.0375	-0.2006	-0.627	-0.0096	-0.2302	0.4022	-0.042	-0.1082	0.6347	-0.0479	0.0466	0.4178	0.0237	0.4622	-1.248	-46.501	67.205

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN B AND RESID 202:490 )	B	202 - 490
2	X-RAY DIFFRACTION	2	( CHAIN B AND RESID 491:709 )	B	491 - 709
3	X-RAY DIFFRACTION	3	( CHAIN B AND RESID 802:803 )	B	802 - 803
4	X-RAY DIFFRACTION	4	( CHAIN C AND RESID 8:97 )	C	8 - 97
5	X-RAY DIFFRACTION	5	( CHAIN C AND RESID 98:240 )	C	98 - 240
6	X-RAY DIFFRACTION	6	( CHAIN C AND RESID 241:344 )	C	241 - 344
7	X-RAY DIFFRACTION	7	( CHAIN C AND RESID 345:490 )	C	345 - 490
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 491:592 )	C	491 - 592
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 593:709 )	C	593 - 709
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 802:803 )	C	802 - 803
11	X-RAY DIFFRACTION	11	( CHAIN D AND RESID 10:282 )	D	10 - 282
12	X-RAY DIFFRACTION	12	( CHAIN D AND RESID 283:455 )	D	283 - 455
13	X-RAY DIFFRACTION	13	( CHAIN D AND RESID 456:709 )	D	456 - 709
14	X-RAY DIFFRACTION	14	( CHAIN D AND RESID 802:803 )	D	802 - 803
15	X-RAY DIFFRACTION	15	( CHAIN A AND RESID 8:97 )	A	8 - 97
16	X-RAY DIFFRACTION	16	( CHAIN A AND RESID 98:240 )	A	98 - 240
17	X-RAY DIFFRACTION	17	( CHAIN A AND RESID 241:344 )	A	241 - 344
18	X-RAY DIFFRACTION	18	( CHAIN A AND RESID 345:490 )	A	345 - 490
19	X-RAY DIFFRACTION	19	( CHAIN A AND RESID 491:708 )	A	491 - 708
20	X-RAY DIFFRACTION	20	( CHAIN A AND RESID 802:803 )	A	802 - 803
21	X-RAY DIFFRACTION	21	( CHAIN B AND RESID 9:201 )	B	9 - 201

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 161 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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