PDB-9gnd: KvPepIH62A mutant in complex with F420,F420-dependent oxidoreductase

ID or keywords:

Entry

Database: PDB / ID: 9gnd

Title

KvPepIH62A mutant in complex with F420,F420-dependent oxidoreductase

Components

Putative F420-dependent oxidoreductase

Keywords

BIOSYNTHETIC PROTEIN / KvPepIH62A mutant in complex with F420 / 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 / COENZYME F420 / Putative F420-dependent oxidoreductase

Function and homology information

Biological species

Streptomyces (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 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	Sep 2, 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	9gnd.cif.gz	228.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9gnd.ent.gz	180.9 KB	Display	PDB format
PDBx/mmJSON format	9gnd.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/gn/9gnd ftp://data.pdbj.org/pub/pdb/validation_reports/gn/9gnd	HTTPS FTP

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Related structure data

Related structure data	9g64C 9gkhC 9gm0C 9gncC 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 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	56.520, 94.271, 110.640
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: 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.: 422 / 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: 2.23 Å³/Da / Density % sol: 44.76 %
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: Dec 11, 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: 1.8→48.48 Å / Num. obs: 55564 / % possible obs: 99.9 % / Redundancy: 26.3 % / CC_1/2: 0.998 / Net I/σ(I): 12.3
Reflection shell	Resolution: 1.8→1.84 Å / Num. unique obs: 3272 / CC_1/2: 0.82

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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: 1.8→48.48 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2042	2837	5.16 %
R_work	0.166	-	-
obs	0.168	55027	99.03 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→48.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4104	0	53	422	4579

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	4232
X-RAY DIFFRACTION	f_angle_d	0.998	5766
X-RAY DIFFRACTION	f_dihedral_angle_d	7.56	610
X-RAY DIFFRACTION	f_chiral_restr	0.057	681
X-RAY DIFFRACTION	f_plane_restr	0.02	746

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 (%)
1.8-1.83	0.2521	145	0.2166	2601	X-RAY DIFFRACTION	100
1.83-1.86	0.2447	134	0.2102	2602	X-RAY DIFFRACTION	100
1.86-1.9	0.2173	142	0.1876	2589	X-RAY DIFFRACTION	100
1.9-1.94	0.2458	160	0.1894	2590	X-RAY DIFFRACTION	100
1.94-1.98	0.2235	132	0.1936	2577	X-RAY DIFFRACTION	100
1.98-2.03	0.2495	148	0.1836	2596	X-RAY DIFFRACTION	99
2.03-2.08	0.2013	139	0.1715	2570	X-RAY DIFFRACTION	99
2.08-2.13	0.2242	141	0.1647	2529	X-RAY DIFFRACTION	97
2.13-2.2	0.2079	143	0.1556	2620	X-RAY DIFFRACTION	100
2.2-2.27	0.2063	122	0.1561	2623	X-RAY DIFFRACTION	100
2.27-2.35	0.211	135	0.1535	2623	X-RAY DIFFRACTION	100
2.35-2.44	0.2103	139	0.1565	2614	X-RAY DIFFRACTION	100
2.44-2.55	0.197	144	0.1548	2624	X-RAY DIFFRACTION	100
2.55-2.69	0.2042	126	0.162	2649	X-RAY DIFFRACTION	100
2.69-2.86	0.1942	147	0.1616	2574	X-RAY DIFFRACTION	99
2.86-3.08	0.1902	152	0.1704	2527	X-RAY DIFFRACTION	96
3.08-3.39	0.2162	142	0.1641	2652	X-RAY DIFFRACTION	100
3.39-3.88	0.1775	145	0.1562	2657	X-RAY DIFFRACTION	99
3.88-4.88	0.1679	148	0.142	2670	X-RAY DIFFRACTION	98
4.88-48.48	0.2338	153	0.1913	2703	X-RAY DIFFRACTION	95

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	2.0778	1.6052	0.7792	3.3123	0.6722	1.0756	-0.0395	0.0533	0.0479	-0.3633	0.0783	0.0372	0.0166	0.0836	-0.078	0.2214	0.0082	0.0322	0.1807	0.0142	0.1836	-11.2065	-12.4317	7.4045
2	1.454	0.1534	-0.1752	1.9216	-0.0462	2.3735	0.0739	0.0354	0.1701	-0.0317	0.007	0.0997	-0.088	-0.2062	-0.0817	0.1559	0.0006	0.0068	0.1514	-0.0044	0.1952	-15.3941	-20.4988	17.8034
3	8.5522	-4.0833	1.4774	4.1413	-0.0799	3.0766	0.0024	-0.345	-0.2986	0.1523	0.0466	0.3468	0.1301	-0.3248	-0.0419	0.2542	-0.0304	0.0173	0.2168	-0.0116	0.229	-20.1894	-19.4823	30.8695
4	0.7781	-0.8284	-0.9385	4.7142	0.2672	1.3364	0.0786	0.1436	-0.1787	-0.1069	-0.0444	0.4956	0.0141	-0.1997	-0.0899	0.1975	-0.0227	-0.0073	0.2313	-0.0317	0.2315	-18.9486	-8.4047	25.7497
5	7.201	-3.5711	4.5339	6.4854	-4.2078	6.4008	-0.0091	-0.1675	0.0908	0.3909	-0.0773	-0.1597	-0.2242	0.1734	0.0432	0.207	0.0038	0.0051	0.216	-0.0648	0.161	-15.2463	-0.3064	32.7879
6	2.9942	-2.0899	2.4522	3.9315	-2.3088	4.7992	-0.113	0.062	0.166	-0.4353	0.0543	0.0796	-0.4341	-0.2409	0.0283	0.338	-0.0133	-0.0087	0.2089	-0.0165	0.2204	-19.6993	6.9551	11.4262
7	2.3031	-1.8194	0.6686	3.1928	-1.2849	4.6635	-0.0653	-0.0461	0.0658	-0.1239	0.0925	-0.0006	-0.3523	-0.3298	-0.0068	0.2522	-0.0252	0.0213	0.1637	-0.02	0.2032	-16.5381	9.0797	16.3491
8	2.7846	-1.4965	-1.9043	7.568	-1.6936	7.0269	0.0519	0.0576	0.1525	-0.5068	-0.0451	-0.1502	0.0591	0.1492	0.107	0.24	-0.0039	0.0599	0.1393	-0.0156	0.1516	-10.4035	-0.5604	8.3206
9	1.0633	0.8773	0.457	3.0101	1.5449	3.0211	-0.0027	0.0646	-0.1688	0.1668	0.1052	-0.3387	0.0552	0.2516	-0.0888	0.1763	-0.0023	-0.0152	0.2034	0.0285	0.2281	-30.8106	-7.8176	-9.689
10	2.6801	0.0659	-0.2056	1.6514	0.411	0.9868	0.0636	-0.0895	-0.0136	0.118	-0.0622	-0.0982	0.0642	0.0391	-0.0026	0.1939	-0.0019	-0.004	0.1425	0.0221	0.1583	-41.9412	-13.6902	-8.4292
11	6.107	-4.0437	-4.0828	4.1476	1.4979	5.0341	0.364	0.2327	0.3748	-0.4762	-0.2174	-0.2992	-0.3027	0.3688	-0.1412	0.2233	0.0167	0.0154	0.2324	0.0765	0.1944	-47.9722	-5.703	-27.8744
12	1.4168	-0.0237	1.64	2.5914	0.1491	2.0753	0.0434	-0.058	0.0597	0.0052	-0.066	0.0827	-0.0765	-0.0659	0.0108	0.1568	0.0283	0.0449	0.2124	0.0122	0.1627	-51.5055	-1.1187	-11.6782
13	5.9155	0.7545	-2.0273	5.6425	-2.6784	7.2387	-0.038	-0.1219	0.343	0.1648	-0.0863	0.3981	-0.1208	-0.3751	0.139	0.221	0.0362	0.0318	0.1674	-0.0515	0.253	-51.8548	11.0577	-5.9384
14	3.714	1.8418	-1.1568	1.7409	-0.2562	2.6913	-0.0813	0.5066	0.4521	-0.1321	0.2546	0.0142	-0.5498	0.2592	-0.1857	0.2814	-0.0695	0.0161	0.2718	0.0511	0.2383	-29.9831	13.6979	-11.6332
15	4.3474	0.4753	0.8467	4.3035	-1.3064	1.676	-0.0247	0.4788	0.5565	-0.0318	-0.0359	-0.0552	-0.2087	0.0079	0.0264	0.2221	-0.0097	0.0044	0.2015	0.0182	0.2039	-33.4702	16.0239	-8.5192
16	4.4296	-0.1736	-0.829	3.5297	0.3671	1.8083	0.0139	0.1239	-0.1299	0.1175	-0.0086	-0.1877	-0.051	-0.0655	-0.0289	0.1815	-0.016	-0.0169	0.1704	0.0189	0.1849	-28.5339	3.0641	-6.001

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 136 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 137 through 153 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 154 through 200 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 201 through 221 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 222 through 247 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 248 through 284 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 285 through 304 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 25 through 67 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 68 through 118 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 119 through 136 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 137 through 200 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 201 through 221 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 222 through 246 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 247 through 284 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 285 through 304 )

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