PDB-3fmw: The crystal structure of MtmOIV, a Baeyer-Villiger monooxygenase ...

ID or keywords:

Entry

Database: PDB / ID: 3fmw

Title

The crystal structure of MtmOIV, a Baeyer-Villiger monooxygenase from the mithramycin biosynthetic pathway in Streptomyces argillaceus.

Components

Oxygenase

Keywords

OXIDOREDUCTASE /

oxygenase /

mithramycin /

Baeyer-Villiger / flavin binding protein

Function / homology

Function and homology information

Biological species

Streptomyces argillaceus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.89 Å

Authors

Noinaj, N. / Beam, M.P. / Wang, C. / Rohr, J.

Citation

Journal: Biochemistry / Year: 2009
Title: Crystal structure of Baeyer-Villiger monooxygenase MtmOIV, the key enzyme of the mithramycin biosynthetic pathway .
Authors: Beam, M.P. / Bosserman, M.A. / Noinaj, N. / Wehenkel, M. / Rohr, J.

History

Deposition	Dec 22, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 5, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 6, 2023	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 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3fmw.cif.gz	533.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3fmw.ent.gz	437.2 KB	Display	PDB format
PDBx/mmJSON format	3fmw.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/fm/3fmw ftp://data.pdbj.org/pub/pdb/validation_reports/fm/3fmw	HTTPS FTP

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Related structure data

Related structure data	2qa1S S: Starting model for refinement
Similar structure data	4k5r-2 6j0z-1 4k5s-1 4icy-1 6wuh-d 5kow-1 7835 4k2x-d Search similar-shape structures by Omokage search (details) 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: Oxygenase

B: Oxygenase

C: Oxygenase

hetero molecules

186 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Oxygenase

hetero molecules

C: Oxygenase

hetero molecules

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

2

B: Oxygenase

hetero molecules

B: Oxygenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	145.265, 114.437, 138.563
Angle α, β, γ (deg.)	90.00, 103.03, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A AND (RESSEQ 14:79 OR RESSEQ 81:194 OR RESSEQ...
2	1	1	CHAIN B AND (RESSEQ 14:79 OR RESSEQ 81:194 OR RESSEQ...
3	1	1	CHAIN C AND (RESSEQ 13:79 OR RESSEQ 81:194 OR RESSEQ...

#1: Protein	Oxygenase / Mass: 61263.867 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces argillaceus (bacteria) / Gene: mtmOIV / Plasmid: pRSET-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q194P4
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.05 Å³/Da / Density % sol: 59.71 %
Crystal grow	Temperature: 298 K / pH: 7.5 Details: 0.1 M Na-HEPES pH 7.5, 10%(v/w) PEG 6000 and 5%(v/v) MPD, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2008
Radiation	Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.887→42.563 Å / Num. obs: 48046

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
RESOLVE		phasing
PHENIX	1.4_4	refinement
PDB_EXTRACT	3.006	data extraction
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QA1

2qa1

Resolution: 2.89→29.68 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.57 / Phase error: 34.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.273	2422	5.11 %
R_work	0.235	-	-
obs	0.237	47393	95.4 %

Solvent computation

Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 73.51 Å² / k_sol: 0.25 e/Å³

Displacement parameters

B_iso mean: 119.11 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	13.914 Å²	-0 Å²	-22.214 Å²
2-	-	-12.814 Å²	0 Å²
3-	-	-	-1.1 Å²

Refinement step

Cycle: LAST / Resolution: 2.89→29.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10174	0	167	18	10359

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	10597
X-RAY DIFFRACTION	f_angle_d	0.993	14559
X-RAY DIFFRACTION	f_dihedral_angle_d	15.513	3648
X-RAY DIFFRACTION	f_chiral_restr	0.072	1683
X-RAY DIFFRACTION	f_plane_restr	0.008	1910

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	3159	X-RAY DIFFRACTION	POSITIONAL
1	2	B	3159	X-RAY DIFFRACTION	POSITIONAL	0.049
1	3	C	3230	X-RAY DIFFRACTION	POSITIONAL	0.033

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 (%)
2.89-2.946	0.434	117	0.425	2121	X-RAY DIFFRACTION	78
2.946-3.01	0.426	138	0.407	2545	X-RAY DIFFRACTION	92
3.01-3.08	0.452	137	0.386	2562	X-RAY DIFFRACTION	92
3.08-3.157	0.451	141	0.369	2562	X-RAY DIFFRACTION	93
3.157-3.242	0.375	144	0.336	2573	X-RAY DIFFRACTION	94
3.242-3.338	0.351	141	0.294	2662	X-RAY DIFFRACTION	95
3.338-3.445	0.299	123	0.277	2691	X-RAY DIFFRACTION	97
3.445-3.568	0.309	133	0.241	2692	X-RAY DIFFRACTION	97
3.568-3.711	0.286	135	0.236	2698	X-RAY DIFFRACTION	97
3.711-3.879	0.273	136	0.221	2681	X-RAY DIFFRACTION	98
3.879-4.083	0.248	157	0.209	2712	X-RAY DIFFRACTION	98
4.083-4.338	0.229	149	0.187	2720	X-RAY DIFFRACTION	98
4.338-4.672	0.21	156	0.186	2717	X-RAY DIFFRACTION	98
4.672-5.14	0.24	165	0.183	2746	X-RAY DIFFRACTION	99
5.14-5.879	0.265	137	0.213	2757	X-RAY DIFFRACTION	99
5.879-7.388	0.292	149	0.217	2770	X-RAY DIFFRACTION	99
7.388-29.684	0.205	164	0.197	2762	X-RAY DIFFRACTION	97

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	1.3811	-1.1742	0.1419	1.2356	-0.1892	-0.0935	-0.4036	0.2776	0.1616	0.4841	0.6847	0.3891	-0.4294	0.2059	-0.1237	0.8991	0.3975	0.6333	0.6312	-0.1763	0.601	27.8732	-20.7386	40.6726
2	0.6769	-0.1755	-0.118	0.5763	-0.222	0.435	0.2931	0.4372	-0.3719	0.3274	-0.0144	0.6017	-0.0658	-0.1535	0.1138	-0.8469	-0.004	0.3256	0.3708	-0.0637	0.4868	32.0911	-29.1434	18.9003
3	1.4903	-0.535	-0.3607	0.3855	-0.2086	0.0276	-0.7046	0.232	0.232	0.6423	0.1821	0.015	-1.454	-0.0816	-1.5909	0.4103	0.664	0.6844	0.0803	-0.2486	-0.0205	27.2344	-14.4308	36.9179
4	-1.618	-0.4093	0.1682	1.2287	-0.5877	1.7246	0.2013	-0.7105	-0.5352	-0.128	0.9151	0.9267	0.7221	-0.7317	-0.9434	0.421	0.1073	-0.1368	0.7326	0.3207	1.4487	16.404	-15.3177	4.9732
5	-1.5516	-0.3255	0.7032	0.8483	-0.8287	0.6214	0.0877	-0.1769	-0.3708	0.0529	0.3771	0.8692	0.0736	-0.4995	-0.7386	0.1322	0.9545	-0.196	0.4599	0.4555	1.2337	14.2653	-9.2309	9.548
6	1.0581	-0.3355	-0.5271	2.4601	-0.4053	2.1812	-0.1929	0.0933	0.2173	0.6495	-0.0892	0.0293	-0.8361	-0.267	-0.0296	0.4046	0.0795	0.1745	0.3182	-0.059	0.4217	38.3754	-15.2521	32.1727
7	0.4347	-0.3628	-0.0197	0.186	0.0127	-0.0321	0.0262	0.3786	0.1174	-0.1299	-0.1527	-0.1875	-0.0488	0.1717	-0.2367	-1.3262	0.5114	0.9539	0.3223	-0.2593	-0.0179	39.1519	-15.51	5.5351
8	0.3802	-0.4968	-0.9839	-0.2219	-1.6572	1.1883	0.1023	0.2416	0.394	-0.1863	-0.5953	0.2591	-0.5082	0.2656	0.0594	0.8286	-0.1598	-0.2191	0.4313	-0.0831	0.4753	50.3793	-29.1995	26.7673
9	0.5382	-0.2311	-0.3487	1.2965	-0.3964	1.9217	-0.0378	-0.3105	-0.109	-0.0936	-0.4543	-0.0141	-0.5815	0.3167	0.2053	0.7661	-0.3014	-0.2452	0.7004	0.0985	0.627	52.8273	-35.3131	36.927
10	0.4144	0.177	0.3893	0.7888	0.5989	-0.4819	0.4414	0.1609	0.0533	0.0324	-0.4508	-0.221	0.7023	-0.1015	-0.1195	2.0625	0.3624	-0.2436	1.2491	-0.2356	0.5874	52.7866	-84.4193	27.27
11	0.3252	0.2468	0.3892	0.8845	0.703	-0.6317	0.3802	-0.188	0.2012	0.1683	-0.6018	0.125	1.2467	-0.0067	0.0259	2.1892	-0.2256	-0.3375	0.8182	-0.0545	0.761	44.1967	-76.588	47.6692
12	0.3656	0.3002	0.1226	0.3122	0.7387	0.1144	0.5834	0.2693	-0.57	0.3013	-0.3196	-0.0384	1.0001	-0.2066	-0.1631	2.3659	0.1521	-0.3574	0.7137	-0.2007	0.7716	54.892	-89.8452	31.3649
13	-0.1519	0.5259	0.3006	1.8922	1.6785	1.2662	0.2548	-0.3313	0.009	0.3084	0.2751	-0.0849	1.3903	-0.5279	-0.4443	2.7933	-0.7742	-0.4309	0.9249	0.108	0.8988	38.2994	-97.773	59.1297
14	0.0907	0.2226	0.2333	1.5466	1.4691	1.6654	0.2846	0.3088	-0.411	0.4162	0.4788	-0.0448	1.6251	0.0657	-0.5312	2.8912	-0.6615	-0.5545	0.7017	0.0724	0.9777	41.2864	-103.1859	53.5399
15	0.8005	0.0373	0.3865	0.8362	0.181	1.4108	0.3678	0.0953	-0.1696	0.6214	0.0898	-0.535	1.7765	-0.1886	-0.2148	2.0511	0.3518	-0.4577	0.8044	-0.1075	0.7751	61.3021	-82.899	38.8287
16	0.3412	0.1522	0.4674	0.6267	0.5924	-0.3728	0.3487	-0.0559	-0.064	0.5453	0.0879	0.1876	1.3259	-0.2114	-0.1205	2.1876	-0.1124	-0.4013	0.7234	-0.0501	0.6559	53.3344	-83.6384	64.4596
17	1.2749	1.3076	0.6132	0.5084	0.1945	5.0545	-0.1102	0.2578	0.1382	0.6998	-0.0117	-0.158	1.0482	0.972	0.0084	1.1049	0.0087	-0.244	1.0154	0.1921	0.8104	60.8421	-64.777	45.3384
18	-0.1056	0.4516	-0.2773	0.5288	-0.0439	3.4416	-0.3665	0.0946	0.3003	-0.1575	0.123	0.3246	0.3171	0.5388	0.1582	0.7237	0.026	0.0196	0.9241	0.1576	0.7984	61.5573	-57.8939	35.0493
19	0.6811	0.0812	-0.2309	2.2942	-0.0683	0.4468	1.1735	0.129	0.1728	1.1021	-0.3209	0.0444	0.0561	-0.0439	0.1361	1.029	-0.2847	0.3153	0.9078	-0.2389	0.4475	16.9738	-61.0954	34.1518
20	1.2185	-0.7774	-0.4475	3.0114	-0.2975	0.2131	0.463	0.1994	-0.0393	-0.6742	-0.2798	0.547	0.2887	-0.2996	0.0399	0.155	-0.1627	0.0198	0.5265	-0.3704	0.8184	10.9109	-65.8631	11.0679
21	0.9337	0.3252	-0.5556	2.2677	-0.1914	0.2218	-0.026	0.1297	0.1606	0.641	-0.2694	-0.1551	-0.0791	0.0267	0.1348	1.0773	-0.2477	0.0238	0.4932	-0.1558	0.5201	22.4127	-58.6866	30.3096
22	1.537	0.7195	0.0869	0.7902	1.0264	1.1065	-0.3172	0.4029	0.8853	-1.0907	0.1464	0.8334	-0.4923	-0.5997	0.1151	1.1403	-0.0721	-0.363	0.8312	0.0424	1.2529	19.6782	-46.1608	-0.7432
23	1.2747	0.9776	0.1746	0.731	0.7009	0.497	-0.4512	-0.1691	1.4111	-0.6495	0.2044	0.5285	-0.5792	0.2722	0.0306	1.1134	-0.2064	-0.3577	0.5731	0.001	1.2498	25.2469	-42.1301	4.8742
24	1.2074	0.7029	-0.1944	2.2347	-0.1966	0.3586	0.1484	0.0245	0.0645	0.9406	-0.3988	-0.21	-0.2131	0.1089	0.2598	0.5888	-0.3422	-0.0531	0.441	-0.0653	0.6207	25.2886	-68.9502	24.9392
25	0.9594	-0.9672	-0.5579	0.9071	0.423	0.3704	0.3409	-0.0646	0.1664	-0.1775	-0.2749	-0.0147	-0.3317	0.056	0.2551	-0.3374	0.3145	0.2675	0.4818	-0.24	0.5164	26.2686	-67.6823	-1.7094
26	-0.1678	0.0037	-0.8648	0.5298	-0.432	0.055	0.2013	-0.151	-0.515	0.6792	-0.0862	-0.1564	1.3073	-0.4272	-0.0519	0.8167	-0.502	-0.1941	0.9203	0.0284	0.8186	16.4735	-85.236	18.2396
27	0.1534	0.0287	-0.3313	0.4276	-0.3041	0.8445	0.0502	0.3427	-0.2373	0.2781	-0.0424	0.6695	1.3417	-0.3354	0.0978	1.8413	-0.7645	0.0154	1.1985	-0.0371	1.0713	10.1501	-90.1492	29.5383
28	0.0011	0.0591	0.0862	0.0415	-0.0083	-0.0745	-0.0816	-0.2191	0.1069	0.1388	0.0883	0.1967	-0.107	-0.0906	-0.0353	0.0207	0.4834	0.3989	0.6664	-0.2911	1.3715	25.2747	-15.6103	27.8968
29	-0.3716	0.2277	-0.0045	-0.1801	0.0708	0.4552	-0.1404	0.0052	-0.2076	-0.099	-0.2178	0.0024	0.0999	0.1029	0.0118	2.1301	-0.0258	-0.0882	0.6006	0.0487	0.9221	50.1088	-91.0025	39.2839
30	-0.2146	0.0952	-0.0532	0.2301	0.108	0.0329	0.0298	-0.1038	0.2897	0.545	-0.1816	-0.3728	0.0501	0.0201	-0.0239	0.882	-0.2822	-0.3947	0.7557	0.1404	1.3587	21.3545	-56.3125	21.5523

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and resid 13:46
2	X-RAY DIFFRACTION	2	chain A and resid 47:101
3	X-RAY DIFFRACTION	3	chain A and resid 102:187
4	X-RAY DIFFRACTION	4	chain A and resid 188:214
5	X-RAY DIFFRACTION	5	chain A and resid 215:269
6	X-RAY DIFFRACTION	6	chain A and resid 270:344
7	X-RAY DIFFRACTION	7	chain A and resid 345:387
8	X-RAY DIFFRACTION	8	chain A and resid 388:422
9	X-RAY DIFFRACTION	9	chain A and resid 423:510
10	X-RAY DIFFRACTION	10	chain B and resid 14:46
11	X-RAY DIFFRACTION	11	chain B and resid 47:101
12	X-RAY DIFFRACTION	12	chain B and resid 102:187
13	X-RAY DIFFRACTION	13	chain B and resid 188:214
14	X-RAY DIFFRACTION	14	chain B and resid 215:269
15	X-RAY DIFFRACTION	15	chain B and resid 270:344
16	X-RAY DIFFRACTION	16	chain B and resid 345:387
17	X-RAY DIFFRACTION	17	chain B and resid 388:422
18	X-RAY DIFFRACTION	18	chain B and resid 423:511
19	X-RAY DIFFRACTION	19	chain C and resid 12:46
20	X-RAY DIFFRACTION	20	chain C and resid 47:101
21	X-RAY DIFFRACTION	21	chain C and resid 102:187
22	X-RAY DIFFRACTION	22	chain C and resid 188:214
23	X-RAY DIFFRACTION	23	chain C and resid 215:269
24	X-RAY DIFFRACTION	24	chain C and resid 270:344
25	X-RAY DIFFRACTION	25	chain C and resid 345:387
26	X-RAY DIFFRACTION	26	chain C and resid 388:422
27	X-RAY DIFFRACTION	27	chain C and resid 423:518
28	X-RAY DIFFRACTION	28	chain D
29	X-RAY DIFFRACTION	29	chain E
30	X-RAY DIFFRACTION	30	chain F

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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

-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

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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

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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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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Phasing

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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

+
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)

+
Jul 12, 2017. Major update of PDB

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Yorodumi