PDB-8t3p: Crystal structure of MonC1 (a flavin-dependent monooxygenase)

ID or keywords:

Entry

Database: PDB / ID: 8t3p

Title

Crystal structure of MonC1 (a flavin-dependent monooxygenase)

Components

MonCI

Keywords

OXIDOREDUCTASE / MonC1 / Flavin-dependent monooxygenase

Function / homology

FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / MonCI

Function and homology information

Biological species

Streptomyces virginiae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.9 Å

Authors

Wang, Q. / Mathews, I.I. / Kim, C.Y.

Funding support

United States, 2items

Organization	Grant number	Country
Department of Energy (DOE, United States)	DE-AC02-76SF00515	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P30GM133894	United States

Citation

Journal: Nat Commun / Year: 2023
Title: Triepoxide formation by a flavin-dependent monooxygenase in monensin biosynthesis.
Authors: Wang, Q. / Liu, N. / Deng, Y. / Guan, Y. / Xiao, H. / Nitka, T.A. / Yang, H. / Yadav, A. / Vukovic, L. / Mathews, I.I. / Chen, X. / Kim, C.Y.

History

Deposition	Jun 7, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 8, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8t3p.cif.gz	390.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8t3p.ent.gz	314.1 KB	Display	PDB format
PDBx/mmJSON format	8t3p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t3/8t3p ftp://data.pdbj.org/pub/pdb/validation_reports/t3/8t3p	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (2) #241 - Jan 2020 Twenty Years of Molecules similarity (2)

Deposited unit

A: MonCI

B: MonCI

hetero molecules

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

1

A: MonCI

hetero molecules

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

2

B: MonCI

hetero molecules

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

Unit cell

Length a, b, c (Å)	67.153, 52.353, 141.561
Angle α, β, γ (deg.)	90.00, 93.60, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	MonCI Mass: 55253.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces virginiae (bacteria) / Gene: monC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q846W9
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 709 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 28.5% w/v PEG MME 2000, 0.1M Tris (pH 6.5), 0.1M MOPS (pH 6.8), 4% Glycerol PH range: 6.5-6.8

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2017 Details: Rh coated collimating mirrors, K-B focusing mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Aimless		data scaling
XDS		data reduction
SHELXDE		phasing

Refinement

Method to determine structure:

MAD / Resolution: 1.9→39.72 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2223	3741	5.09 %
R_work	0.1815	-	-
obs	0.1836	73562	94.44 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.9→39.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7114	0	108	709	7931

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7443
X-RAY DIFFRACTION	f_angle_d	0.987	10172
X-RAY DIFFRACTION	f_dihedral_angle_d	10.564	1057
X-RAY DIFFRACTION	f_chiral_restr	0.06	1159
X-RAY DIFFRACTION	f_plane_restr	0.012	1345

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 (%)
1.9-1.92	0.3681	126	0.2851	2611	X-RAY DIFFRACTION	95
1.92-1.95	0.3155	135	0.2715	2600	X-RAY DIFFRACTION	96
1.95-1.98	0.3281	147	0.265	2585	X-RAY DIFFRACTION	95
1.98-2	0.3004	142	0.2504	2599	X-RAY DIFFRACTION	96
2-2.03	0.2636	140	0.2281	2603	X-RAY DIFFRACTION	95
2.03-2.07	0.2839	154	0.2138	2544	X-RAY DIFFRACTION	96
2.07-2.1	0.2386	146	0.2146	2548	X-RAY DIFFRACTION	93
2.1-2.14	0.2507	125	0.2161	2504	X-RAY DIFFRACTION	93
2.14-2.17	0.2426	143	0.2063	2294	X-RAY DIFFRACTION	84
2.17-2.22	0.2373	120	0.2007	2509	X-RAY DIFFRACTION	92
2.22-2.26	0.2469	149	0.2001	2621	X-RAY DIFFRACTION	96
2.26-2.31	0.2575	148	0.2033	2608	X-RAY DIFFRACTION	96
2.31-2.36	0.2442	167	0.203	2628	X-RAY DIFFRACTION	97
2.37-2.42	0.2117	137	0.1962	2595	X-RAY DIFFRACTION	96
2.42-2.49	0.2533	159	0.188	2627	X-RAY DIFFRACTION	95
2.49-2.56	0.2133	144	0.1822	2584	X-RAY DIFFRACTION	97
2.56-2.65	0.2184	145	0.18	2605	X-RAY DIFFRACTION	95
2.65-2.74	0.2659	137	0.1871	2540	X-RAY DIFFRACTION	92
2.74-2.85	0.2682	125	0.1882	2363	X-RAY DIFFRACTION	87
2.85-2.98	0.2592	129	0.1875	2668	X-RAY DIFFRACTION	98
2.98-3.14	0.2466	104	0.185	2720	X-RAY DIFFRACTION	97
3.14-3.33	0.2027	158	0.1722	2654	X-RAY DIFFRACTION	97
3.33-3.59	0.1915	153	0.1636	2639	X-RAY DIFFRACTION	96
3.59-3.95	0.1801	131	0.1533	2587	X-RAY DIFFRACTION	94
3.95-4.52	0.1613	113	0.1359	2550	X-RAY DIFFRACTION	91
4.52-5.69	0.1566	127	0.1516	2722	X-RAY DIFFRACTION	97
5.7-39.72	0.2158	137	0.1708	2713	X-RAY DIFFRACTION	94

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	0.9797	-0.086	-0.0914	0.4454	-0.0169	0.7611	0.0194	0.0499	0.0684	-0.0109	-0.0136	-0.0615	-0.0592	0.195	-0.0004	0.1696	-0.0198	0.0057	0.1273	0.0007	0.1594	52.4807	18.4085	13.7403
2	0.4064	-0.1611	-0.0279	0.7603	0.0082	0.4125	0.0307	0.0119	0.0059	-0.0079	-0.0363	0.1162	-0.0305	-0.0295	0.018	0.2087	-0.0095	0.0088	0.0845	-0.0013	0.1919	30.2553	22.9481	9.9563
3	0.3994	0.0347	-0.0508	0.3268	0.0606	0.617	0.0211	0.0108	-0.0727	-0.0089	-0.0038	0.0289	0.0657	0.0827	-0.0283	0.181	0.0061	0.0039	0.0782	0.0002	0.1732	42.7526	9.5996	17.2104
4	0.7798	0.1074	-0.1447	1.0993	0.0614	0.545	0.0025	-0.1124	0.0148	0.0601	0.0145	0.2103	-0.0449	-0.0641	-0.0294	0.2269	-0.0021	0.0271	0.1539	0.0043	0.2216	25.4279	20.1446	30.0604
5	1.3145	-0.2852	0.8371	1.3037	-0.2618	1.2019	0.0993	-0.4848	-0.3169	-0.0225	-0.0717	0.0815	0.0481	0.0806	-0.0872	0.202	-0.0705	0.008	0.5165	0.1867	0.2971	38.1335	0.4099	48.4395
6	0.3587	0.1263	0.1343	0.3052	-0.3972	0.8144	0.0715	-0.7184	-0.1913	0.2026	-0.0671	-0.0222	-0.0565	0.095	0.0338	0.294	-0.0828	-0.0006	0.9083	0.1111	0.2239	52.5493	5.0728	57.7329
7	0.3848	0.2144	-0.3166	0.235	0.1135	0.9686	0.0409	-0.4643	0.1335	0.0237	-0.0926	0.0345	-0.0429	-0.0239	-0.1876	0.2285	-0.0992	0.0916	0.8157	-0.2095	0.2522	59.5805	17.801	55.4133
8	1.0016	-0.1488	-0.6981	0.4943	-0.1906	0.6655	0.0952	-0.5354	0.0982	0.1005	-0.1106	-0.0295	-0.003	-0.1207	-0.0255	0.2462	-0.074	0.0168	0.7447	-0.0068	0.1746	61.4976	13.2876	54.0691
9	0.6356	-0.2975	-0.2326	1.7181	0.1577	1.9127	-0.0362	-0.6429	-0.4429	0.0259	0.0796	0.0079	0.3098	-0.0107	0.0242	0.3303	-0.0753	-0.0137	0.6845	0.3262	0.5226	37.4665	-9.1393	53.6319
10	0.8644	-0.0658	0.0317	0.2791	-0.0987	0.129	0.0941	-0.598	-0.3845	0.0749	-0.0505	0.0959	0.1072	0.1268	-0.0247	0.3077	-0.0641	-0.0952	0.6058	0.3869	0.4958	50.7654	-10.2419	52.5524
11	0.6115	-0.0154	0.1194	0.282	-0.0023	0.1927	0.1752	-0.6887	-0.132	0.1913	-0.196	-0.0464	0.0655	0.0453	-0.0433	0.3067	-0.1483	-0.0874	1.2588	0.146	0.2772	73.6089	6.0627	62.8082
12	0.6104	-0.3111	-0.2166	0.4702	-0.1002	0.4572	0.1972	-0.6572	-0.3946	0.1397	-0.1111	-0.0072	0.1579	0.218	-0.0838	0.2524	-0.0478	-0.0281	0.4409	0.1731	0.2715	52.8694	-1.8403	46.1736
13	1.1391	-0.4367	0.1332	0.5646	-0.0475	0.8486	0.145	-0.245	-0.6294	-0.0148	-0.1443	-0.103	0.1729	0.309	0.0278	0.2536	0.0472	-0.0509	0.3023	0.1349	0.3872	62.2803	-5.1521	38.8015
14	0.9409	0.6796	0.1229	1.4918	0.2779	1.0055	0.0941	-0.056	0.0613	-0.144	-0.1551	-0.2727	0.065	0.2021	0.0343	0.1973	0.0037	0.0091	0.4008	0.0311	0.2268	75.1428	9.5496	39.5523
15	0.0333	-0.0938	-0.0882	0.5213	0.0376	1.0504	0.0979	-0.5731	0.2482	0.0478	-0.0254	-0.0243	-0.1403	0.2532	-0.1058	0.2331	-0.0574	0.0167	0.6328	-0.0849	0.2615	75.5237	17.2712	44.7473

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 192 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 193 through 276 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 277 through 406 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 407 through 480 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 4 through 35 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 36 through 70 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 71 through 95 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 96 through 126 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 127 through 161 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 162 through 214 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 215 through 286 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 287 through 361 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 362 through 406 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 407 through 435 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 436 through 477 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi