PDB-9gm0: KvPepI F420-dependent oxidoreductase, F420 complex

ID or keywords:

Entry

Database: PDB / ID: 9gm0

Title

KvPepI F420-dependent oxidoreductase, F420 complex

Components

Putative F420-dependent oxidoreductase

Keywords

BIOSYNTHETIC PROTEIN / KvPepi F420-dependent reductase in complex with F420 / Pepstatin biosynthesis

Function / homology

Luciferase-like, F420-dependent oxidoreductase, MSMEG2516, predicted / alkanesulfonate monooxygenase activity / : / alkanesulfonate catabolic process / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / COENZYME F420 / Putative F420-dependent oxidoreductase

Function and homology information

Biological species

Streptomyces (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Mueller, R. / Zhao, H. / Sikandar, A.

Funding support

1items

Citation

Journal: Nat Commun / Year: 2025
Title: Tandem ketone reduction in pepstatin biosynthesis reveals an F 420 H 2 -dependent statine pathway.
Authors: Mo, J. / Sikandar, A. / Zhao, H. / Bashiri, G. / Huo, L. / Empting, M. / Muller, R. / Fu, C.

History

Deposition	Aug 28, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 11, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9gm0.cif.gz	229.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9gm0.ent.gz	181.1 KB	Display	PDB format
PDBx/mmJSON format	9gm0.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/gm/9gm0 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/9gm0	HTTPS FTP

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Related structure data

Related structure data	9g64C 9gkhC 9gncC 9gndC C: citing same article (ref.)
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	#78 - Jun 2006 Luciferase similarity (3)

Deposited unit

A: Putative F420-dependent oxidoreductase

B: Putative F420-dependent oxidoreductase

hetero molecules

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

1

A: Putative F420-dependent oxidoreductase

hetero molecules

defined by author
Evidence: gel filtration
33.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative F420-dependent oxidoreductase

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

Unit cell

Length a, b, c (Å)	56.353, 94.271, 111.024
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Putative F420-dependent oxidoreductase Mass: 33160.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces (bacteria) / Gene: FHX73_11672 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A561UC02
#2: Chemical	ChemComp-F42 / COENZYME F420 Mass: 773.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₉H₃₆N₅O₁₈P / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.22 Å³/Da / Density % sol: 44.68 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 30% (w/v) PEG 4000, 0.2 M Sodium acetate and 0.1 M Tris-Cl pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 29, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03 Å / Relative weight: 1
Reflection	Resolution: 1.65→48.37 Å / Num. obs: 71956 / % possible obs: 100 % / Redundancy: 13.4 % / CC_1/2: 0.99 / Net I/σ(I): 17.1
Reflection shell	Resolution: 1.65→1.68 Å / Num. unique obs: 3513 / CC_1/2: 0.703

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.1_4122: ???)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→48.37 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1811	3652	5.08 %
R_work	0.1568	-	-
obs	0.1581	71860	99.94 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.65→48.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4118	0	53	524	4695

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4248
X-RAY DIFFRACTION	f_angle_d	1.062	5787
X-RAY DIFFRACTION	f_dihedral_angle_d	6.878	602
X-RAY DIFFRACTION	f_chiral_restr	0.058	681
X-RAY DIFFRACTION	f_plane_restr	0.024	749

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 (%)
1.65-1.67	0.2924	131	0.2488	2594	X-RAY DIFFRACTION	100
1.67-1.69	0.2439	150	0.2234	2581	X-RAY DIFFRACTION	100
1.69-1.72	0.2316	124	0.1968	2606	X-RAY DIFFRACTION	100
1.72-1.74	0.2229	113	0.1828	2624	X-RAY DIFFRACTION	100
1.74-1.77	0.2004	130	0.1702	2613	X-RAY DIFFRACTION	100
1.77-1.8	0.1953	145	0.1636	2575	X-RAY DIFFRACTION	100
1.8-1.83	0.2167	142	0.1615	2572	X-RAY DIFFRACTION	100
1.83-1.87	0.1967	158	0.1592	2592	X-RAY DIFFRACTION	100
1.87-1.9	0.1952	132	0.1578	2595	X-RAY DIFFRACTION	100
1.9-1.94	0.1962	132	0.1585	2611	X-RAY DIFFRACTION	100
1.94-1.98	0.1879	162	0.1665	2564	X-RAY DIFFRACTION	100
1.98-2.03	0.1694	147	0.1462	2607	X-RAY DIFFRACTION	100
2.03-2.08	0.1693	154	0.1426	2595	X-RAY DIFFRACTION	100
2.08-2.14	0.1663	125	0.1385	2606	X-RAY DIFFRACTION	100
2.14-2.2	0.1825	143	0.1402	2631	X-RAY DIFFRACTION	100
2.2-2.27	0.1741	139	0.1362	2594	X-RAY DIFFRACTION	100
2.27-2.35	0.1698	132	0.1398	2645	X-RAY DIFFRACTION	100
2.35-2.44	0.1725	138	0.1458	2615	X-RAY DIFFRACTION	100
2.44-2.56	0.1851	147	0.1492	2626	X-RAY DIFFRACTION	100
2.56-2.69	0.1469	139	0.152	2624	X-RAY DIFFRACTION	100
2.69-2.86	0.1838	137	0.1523	2627	X-RAY DIFFRACTION	100
2.86-3.08	0.1783	147	0.1574	2634	X-RAY DIFFRACTION	100
3.08-3.39	0.1663	142	0.1633	2666	X-RAY DIFFRACTION	100
3.39-3.88	0.1805	138	0.1477	2670	X-RAY DIFFRACTION	100
3.88-4.89	0.1578	156	0.1409	2706	X-RAY DIFFRACTION	100
4.89-48.37	0.2124	149	0.1903	2835	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	0.2794	-0.0008	0.1074	1.1751	0.2908	0.4935	0.0177	-0.0184	0.0342	-0.0619	0.0058	-0.0189	-0.0226	-0.0097	-0.0216	0.1381	-0.0022	0.0127	0.1631	0.0001	0.1691	-14.6474	-16.4665	18.2626
2	1.6306	-0.0583	0.1258	1.7252	-0.2671	1.7337	0.1836	0.0763	-0.2884	-0.1533	0.0214	0.2552	0.0065	-0.0929	-0.194	0.1578	0.0156	-0.0196	0.173	-0.0313	0.1875	-20.409	-0.6821	27.8124
3	1.1398	-0.5526	0.5568	1.2387	-0.3674	1.5775	-0.059	-0.0147	0.0929	-0.2496	0.0753	0.0044	-0.2516	-0.1567	-0.012	0.2446	-0.007	0.0132	0.1772	-0.0099	0.1868	-17.8273	8.1657	14.1735
4	0.472	0.0563	-1.0718	3.312	-0.9767	3.1274	0.0278	0.0071	0.0617	-0.3959	0.0034	-0.1488	-0.0021	0.0263	0.003	0.2716	-0.0055	0.0646	0.1844	-0.0138	0.2088	-10.3636	-0.5217	8.181
5	0.5757	0.4297	0.2141	1.1981	0.4171	1.3043	0.0022	0.0499	-0.1072	0.1027	0.0575	-0.246	-0.0033	0.1311	-0.0388	0.1581	-0.0084	-0.031	0.189	0.0136	0.2038	-30.8998	-8.0386	-10.0541
6	0.7058	-0.0461	-0.2394	0.7863	0.0339	0.4986	-0.0049	-0.0473	-0.0288	0.1506	-0.0042	-0.0891	-0.0222	0.0314	0.006	0.1866	-0.0011	-0.0146	0.1579	0.0114	0.1707	-41.8925	-13.9723	-8.6878
7	2.0398	-1.1469	-1.2022	1.461	0.5586	1.6425	0.1349	0.1671	0.2446	-0.1592	-0.1029	-0.0467	-0.2149	0.1824	-0.0063	0.2071	0.0273	0.017	0.2089	0.0427	0.1765	-47.759	-6.031	-28.0676
8	0.7551	-0.1819	0.3668	1.0151	-0.9026	1.5177	0.0684	-0.0627	-0.0101	0.012	-0.0266	0.0403	0.0431	-0.1122	-0.0292	0.1835	0.0122	0.0091	0.1857	0.0171	0.1699	-53.3215	-6.1842	-12.2158
9	0.8754	-0.1674	0.9829	2.1643	0.3329	1.2227	0.0563	0.176	0.1526	-0.119	-0.1619	-0.0027	-0.0277	0.0911	0.1119	0.1927	0.023	0.0164	0.2276	0.023	0.1804	-48.8867	4.8558	-11.5307
10	3.1798	0.7003	-0.8645	2.909	-1.5384	3.9381	-0.0748	-0.1799	0.3257	0.2026	-0.1279	0.2849	-0.0759	-0.2597	0.1934	0.2434	0.0236	0.0351	0.212	-0.0324	0.2567	-51.7121	10.796	-6.1945
11	2.7264	1.4008	-0.8284	1.297	-0.1445	0.9152	-0.0799	0.1203	0.1034	-0.0004	0.1305	-0.1594	-0.1859	0.1906	-0.0165	0.2185	-0.0517	0.006	0.2559	-0.0019	0.2223	-32.6764	8.5432	-8.847
12	4.7413	-0.5068	2.2463	1.5578	-1.2672	5.6462	0.2424	0.7783	0.2529	-0.1617	0.2263	0.1445	-0.4153	-0.3774	-0.3391	0.3995	-0.0751	0.0224	0.5441	0.1752	0.4099	-28.2278	20.5761	-18.7584
13	2.8344	0.2454	-0.0324	0.8133	0.1849	0.8861	0.0831	0.1761	0.3917	0.1067	-0.0447	-0.0169	-0.1947	0.0619	-0.0055	0.2563	-0.0404	0.0067	0.2183	-0.0008	0.2367	-33.4004	14.8987	-5.9057
14	2.2487	0.0766	-0.461	1.3461	0.1249	0.5632	0.0228	0.1583	-0.1792	0.1103	-0.0197	-0.0891	-0.0858	-0.0629	-0.0128	0.1984	-0.0267	-0.03	0.1922	0.0079	0.2016	-28.4612	2.7625	-6.1996

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 25 through 182 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 183 through 221 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 222 through 284 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 285 through 304 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 25 through 67 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 68 through 118 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 119 through 136 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 137 through 166 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 167 through 200 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 201 through 221 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 222 through 236 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 237 through 252 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 253 through 284 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 285 through 304 )

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