PDB-9gkh: KvPepIH62A mutant,F420-dependent oxidoreductase

ID or keywords:

Entry

Database: PDB / ID: 9gkh

Title

KvPepIH62A mutant,F420-dependent oxidoreductase

Components

Putative F420-dependent oxidoreductase

Keywords

BIOSYNTHETIC PROTEIN / KvPepIH62A mutant / F420-dependent oxidoreductase

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 / Putative F420-dependent oxidoreductase

Function and homology information

Biological species

Streptomyces (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 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 24, 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	9gkh.cif.gz	219.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9gkh.ent.gz	174.6 KB	Display	PDB format
PDBx/mmJSON format	9gkh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9gkh_validation.pdf.gz	435.1 KB	Display	wwPDB validaton report
Full document	9gkh_full_validation.pdf.gz	437.4 KB	Display
Data in XML	9gkh_validation.xml.gz	27.4 KB	Display
Data in CIF	9gkh_validation.cif.gz	38.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gk/9gkh ftp://data.pdbj.org/pub/pdb/validation_reports/gk/9gkh	HTTPS FTP

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Related structure data

Related structure data	9g64C 9gm0C 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

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

1

A: Putative F420-dependent oxidoreductase

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

2

B: Putative F420-dependent oxidoreductase

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

Unit cell

Length a, b, c (Å)	56.213, 94.283, 110.823
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: 33093.656 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H₂O
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: 44.56 %
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: Oct 30, 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: 1.7→48.28 Å / Num. obs: 65590 / % possible obs: 100 % / Redundancy: 34.3 % / CC_1/2: 1 / Net I/σ(I): 28.5
Reflection shell	Resolution: 1.7→1.73 Å / Num. unique obs: 3416 / CC_1/2: 0.89

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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: 1.7→48.28 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1942	3296	5.03 %
R_work	0.1731	-	-
obs	0.1742	65512	99.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.7→48.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4081	0	0	380	4461

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	4151
X-RAY DIFFRACTION	f_angle_d	1.073	5647
X-RAY DIFFRACTION	f_dihedral_angle_d	7.251	589
X-RAY DIFFRACTION	f_chiral_restr	0.061	669
X-RAY DIFFRACTION	f_plane_restr	0.033	735

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 (%)
1.7-1.72	0.3353	140	0.2704	2547	X-RAY DIFFRACTION	100
1.72-1.75	0.2876	134	0.2338	2574	X-RAY DIFFRACTION	100
1.75-1.78	0.2287	135	0.2057	2531	X-RAY DIFFRACTION	100
1.78-1.81	0.2335	144	0.1938	2559	X-RAY DIFFRACTION	100
1.81-1.84	0.2033	140	0.1776	2555	X-RAY DIFFRACTION	100
1.84-1.87	0.2049	144	0.1699	2545	X-RAY DIFFRACTION	100
1.87-1.91	0.2133	124	0.1688	2566	X-RAY DIFFRACTION	100
1.91-1.95	0.2135	147	0.1812	2585	X-RAY DIFFRACTION	100
1.95-1.99	0.2145	125	0.1928	2569	X-RAY DIFFRACTION	100
1.99-2.03	0.2378	145	0.1799	2555	X-RAY DIFFRACTION	100
2.03-2.09	0.1977	148	0.166	2561	X-RAY DIFFRACTION	100
2.09-2.14	0.2129	137	0.1623	2582	X-RAY DIFFRACTION	100
2.14-2.2	0.1771	145	0.1572	2545	X-RAY DIFFRACTION	100
2.2-2.28	0.1628	138	0.155	2582	X-RAY DIFFRACTION	100
2.28-2.36	0.1639	115	0.1532	2629	X-RAY DIFFRACTION	100
2.36-2.45	0.2136	118	0.1645	2601	X-RAY DIFFRACTION	100
2.45-2.56	0.2198	134	0.1721	2591	X-RAY DIFFRACTION	100
2.56-2.7	0.1747	148	0.1732	2587	X-RAY DIFFRACTION	100
2.7-2.87	0.1812	123	0.1779	2608	X-RAY DIFFRACTION	100
2.87-3.09	0.1977	145	0.1797	2603	X-RAY DIFFRACTION	100
3.09-3.4	0.2201	135	0.1813	2625	X-RAY DIFFRACTION	100
3.4-3.89	0.1733	146	0.1628	2641	X-RAY DIFFRACTION	100
3.89-4.9	0.1673	142	0.1478	2666	X-RAY DIFFRACTION	100
4.9-48.28	0.1963	144	0.1988	2809	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	0.4822	-0.2246	0.1534	0.7455	0.1144	0.0954	0.0077	-0.0573	-0.0488	-0.2595	0.0007	-0.0691	-0.0002	0.022	0.0001	0.2512	-0.0107	0.0303	0.2147	0.0101	0.2054	-11.2067	-12.1924	7.617
2	0.1991	-0.0313	0.2806	0.3521	0.1539	0.6499	0.0509	-0.0072	0.089	-0.032	0.0115	-0.0779	-0.0431	0.0007	0.0001	0.2023	-0.0014	0.0233	0.2107	-0.0002	0.2393	-9.8516	-20.5755	16.801
3	0.2881	-0.2847	-0.1754	0.5601	0.5223	0.5239	0.1061	-0.0958	0.1671	0.1715	-0.1497	0.1815	0.0859	-0.1604	0.0001	0.247	-0.0098	0.0294	0.2838	0.0085	0.3021	-25.941	-19.2175	25.5279
4	0.1138	0.063	0.0117	0.3866	0.3577	0.3348	0.1532	0.0393	-0.0494	0.0841	-0.1206	0.1154	0.0707	-0.0289	-0.0001	0.2498	0.0009	0.0264	0.2351	-0.0198	0.2638	-14.9312	-12.5641	29.3377
5	0.0205	-0.0521	-0.0409	0.1149	0.1724	0.3106	0.0973	-0.0396	-0.2219	-0.2649	0.0158	0.221	0.0706	-0.1631	0.0005	0.2395	0.0088	-0.0174	0.2895	-0.0254	0.2548	-20.9092	-2.0578	21.8784
6	0.1946	0.2233	0.0025	0.4209	-0.1704	0.165	-0.0162	-0.0507	0.0124	0.2035	-0.0203	-0.0291	-0.1877	0.0998	-0.0004	0.2331	0.0112	-0.0069	0.2631	-0.0283	0.203	-15.1889	0.0189	32.4698
7	0.2364	-0.1507	0.1864	0.0971	-0.0834	0.2135	-0.1611	-0.1059	0.1098	-0.0218	0.126	-0.0221	-0.2245	-0.1611	-0	0.2932	0.003	-0.0225	0.2414	-0.0008	0.2622	-19.2127	7.1033	11.2643
8	0.275	-0.3521	0.1583	0.6309	-0.5304	0.6136	-0.068	-0.0369	0.1127	-0.0573	0.0712	-0.012	-0.16	-0.1475	0.0001	0.2255	-0.0162	0.006	0.2282	-0.0113	0.232	-17.284	9.4156	15.4056
9	0.2826	-0.3922	-0.1538	0.5073	0.2165	0.1695	-0.0063	0.0141	0.0664	-0.1961	0.0462	-0.072	0.1641	0.0185	-0	0.283	-0.0316	0.0323	0.2253	-0.0145	0.2297	-10.8443	-0.5004	9.4167
10	0.3867	0.4785	0.1334	0.987	-0.0397	0.3802	0.0319	0.0368	-0.0963	0.0319	0.0116	-0.1915	-0.0668	-0.0486	-0.0001	0.1957	-0.0014	-0.0305	0.2238	-0.0011	0.2412	-31.0218	-7.7328	-9.6132
11	0.5801	-0.0399	-0.5057	0.5207	0.0656	0.4464	0.0258	-0.0168	0.0207	0.0613	-0.0273	-0.098	0.0218	0.0049	-0	0.2331	-0.0058	-0.0282	0.1959	0.0166	0.2147	-41.8631	-13.8324	-8.5297
12	0.19	-0.1323	0.0383	0.1324	0.0426	0.1111	0.0486	0.1048	0.1663	-0.1633	-0.0126	-0.1413	-0.1813	0.1584	-0	0.2824	0.0424	0.0137	0.2937	0.0347	0.2385	-47.938	-6.0658	-28.0739
13	0.195	-0.0188	0.0784	0.1564	-0.1046	0.0784	0.0686	-0.0429	-0.0054	-0.0526	-0.1057	0.0602	0.2075	0.07	0.0001	0.2073	0.015	0.0039	0.2562	0.0079	0.2121	-56.0352	-6.4285	-15.3786
14	0.4015	0.0197	0.3595	0.6521	0.4013	0.5097	0.0359	-0.0242	0.0586	-0.0151	-0.0532	0.0281	-0.0515	-0.0601	-0	0.2223	0.011	0.0114	0.2325	0.0188	0.2167	-49.0969	1.2308	-10.3234
15	0.4031	-0.2856	0.0768	0.6331	0.3516	0.3896	0.0161	-0.2472	0.2927	0.2191	-0.1673	0.1845	-0.1304	-0.1679	-0.0007	0.2496	0.0214	0.0322	0.2435	-0.0113	0.2737	-51.7864	10.8543	-6.3622
16	0.4354	0.1844	0.2391	0.1993	0.3615	0.5968	0.0571	0.3823	0.3022	0.0128	0.1154	0.0504	-0.2522	0.0107	0.0005	0.2654	-0.0465	0.0339	0.2914	0.0345	0.2909	-29.9074	13.4356	-11.901
17	0.3504	0.0367	-0.0947	0.2061	-0.0116	0.0577	0.1553	0.5867	0.3396	-0.1629	-0.0504	-0.1947	-0.1779	0.1419	0.0009	0.3469	-0.0027	0.0348	0.401	0.098	0.3463	-31.885	17.9985	-15.2564
18	0.12	0.0802	0.0884	0.2071	-0.0269	0.1064	-0.0039	-0.0231	0.2667	0.1157	0.0289	0.0068	-0.1278	0.0121	0.0001	0.261	-0.0094	0.0106	0.2143	-0.0147	0.2281	-34.3313	14.1348	-2.0698
19	0.2009	0.0948	-0.1033	0.4609	-0.0419	0.0519	-0.0069	0.0582	-0.0995	0.032	0.0129	-0.002	-0.0748	-0.0903	-0	0.2394	-0.0222	-0.005	0.2386	-0.002	0.2277	-29.6732	3.4347	-6.2097

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 25 through 67 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 68 through 118 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 119 through 153 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 154 through 176 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 177 through 200 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 201 through 221 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 222 through 246 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 247 through 282 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 283 through 303 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 25 through 67 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 68 through 118 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 119 through 136 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 137 through 153 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 154 through 200 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 201 through 221 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 222 through 246 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 247 through 266 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 267 through 282 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 283 through 303 )

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