PDB-9gnc: KvPepIY122A mutant in complex with F420, F420-dependent oxidoreductase

ID or keywords:

Entry

Database: PDB / ID: 9gnc

Title

KvPepIY122A mutant in complex with F420, F420-dependent oxidoreductase

Components

Putative F420-dependent oxidoreductase

Keywords

BIOSYNTHETIC PROTEIN / KvPepIY122A 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: 1.65 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	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	9gnc.cif.gz	231 KB	Display	PDBx/mmCIF format
PDB format	pdb9gnc.ent.gz	182.3 KB	Display	PDB format
PDBx/mmJSON format	9gnc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9gnc_validation.pdf.gz	738.2 KB	Display	wwPDB validaton report
Full document	9gnc_full_validation.pdf.gz	741.3 KB	Display
Data in XML	9gnc_validation.xml.gz	31.3 KB	Display
Data in CIF	9gnc_validation.cif.gz	44.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gn/9gnc ftp://data.pdbj.org/pub/pdb/validation_reports/gn/9gnc	HTTPS FTP

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Related structure data

Related structure data	9g64C 9gkhC 9gm0C 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

66.2 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
33.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative F420-dependent oxidoreductase

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

Unit cell

Length a, b, c (Å)	56.310, 94.593, 110.756
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: 32696.227 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.: 569 / 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: 2.31 Å³/Da / Density % sol: 46.73 %
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: 1.65→48.39 Å / Num. obs: 71529 / % possible obs: 99.5 % / Redundancy: 34.3 % / CC_1/2: 0.99 / Net I/σ(I): 21.2
Reflection shell	Resolution: 1.65→1.68 Å / Num. unique obs: 3484 / CC_1/2: 0.847

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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→48.39 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1884	3635	5.09 %
R_work	0.1571	-	-
obs	0.1587	71428	99.34 %

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→48.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4157	0	0	569	4726

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	4232
X-RAY DIFFRACTION	f_angle_d	1.324	5765
X-RAY DIFFRACTION	f_dihedral_angle_d	7.45	609
X-RAY DIFFRACTION	f_chiral_restr	0.076	681
X-RAY DIFFRACTION	f_plane_restr	0.016	747

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	0.2436	129	0.203	2557	X-RAY DIFFRACTION	99
1.67-1.69	0.227	151	0.1945	2578	X-RAY DIFFRACTION	100
1.69-1.72	0.2909	124	0.1824	2567	X-RAY DIFFRACTION	98
1.72-1.74	0.1843	117	0.1641	2581	X-RAY DIFFRACTION	100
1.74-1.77	0.1809	129	0.1564	2588	X-RAY DIFFRACTION	98
1.77-1.8	0.1828	141	0.155	2571	X-RAY DIFFRACTION	100
1.8-1.83	0.211	147	0.1629	2542	X-RAY DIFFRACTION	99
1.83-1.87	0.2131	150	0.1616	2594	X-RAY DIFFRACTION	100
1.87-1.9	0.1756	140	0.1585	2568	X-RAY DIFFRACTION	99
1.9-1.94	0.1888	127	0.1574	2619	X-RAY DIFFRACTION	99
1.94-1.98	0.2105	164	0.1534	2549	X-RAY DIFFRACTION	100
1.98-2.03	0.2032	133	0.1474	2534	X-RAY DIFFRACTION	97
2.03-2.08	0.1791	156	0.1455	2610	X-RAY DIFFRACTION	100
2.08-2.14	0.1746	124	0.1436	2583	X-RAY DIFFRACTION	100
2.14-2.2	0.187	148	0.1485	2616	X-RAY DIFFRACTION	100
2.2-2.27	0.2154	133	0.1462	2590	X-RAY DIFFRACTION	100
2.27-2.35	0.1764	132	0.1445	2639	X-RAY DIFFRACTION	100
2.35-2.44	0.1878	140	0.1466	2617	X-RAY DIFFRACTION	100
2.44-2.56	0.197	145	0.1521	2636	X-RAY DIFFRACTION	100
2.56-2.69	0.1649	140	0.1542	2622	X-RAY DIFFRACTION	100
2.69-2.86	0.2052	136	0.1572	2581	X-RAY DIFFRACTION	98
2.86-3.08	0.188	147	0.1607	2618	X-RAY DIFFRACTION	99
3.08-3.39	0.1849	139	0.1594	2670	X-RAY DIFFRACTION	100
3.39-3.88	0.1702	140	0.1495	2675	X-RAY DIFFRACTION	100
3.88-4.89	0.1649	155	0.1401	2703	X-RAY DIFFRACTION	100
4.89-48.39	0.2031	148	0.187	2785	X-RAY DIFFRACTION	98

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	0.3234	0.1657	0.1929	1.7361	0.184	0.7035	0.0217	-0.019	0.035	-0.0549	-0.0034	0.0335	0.011	-0.0186	-0.017	0.1051	-0.0003	0.0118	0.1255	0.0001	0.14	-14.5775	-16.6364	18.2045
2	2.6105	0.4183	-0.5121	3.2051	-0.2485	3.9262	0.1587	0.1099	-0.3601	-0.1385	0.093	0.4451	0.06	-0.2633	-0.219	0.1506	0.0024	-0.0259	0.163	-0.0408	0.1978	-20.1521	-0.7603	27.6075
3	1.7389	-0.9473	0.5611	2.6977	-0.4941	3.3232	-0.0237	0.0616	0.1327	-0.3232	0.0069	-0.0113	-0.2869	-0.2169	0.0264	0.1834	-0.0246	0.0222	0.1346	-0.0115	0.153	-16.0359	6.0218	12.7915
4	0.8617	0.5862	0.437	2.8621	1.5834	3.212	0.006	0.0222	-0.1565	0.133	0.0884	-0.303	0.0499	0.1273	-0.1027	0.1239	-0.0112	-0.0189	0.15	0.0273	0.1687	-30.8831	-7.9708	-10.0227
5	1.7947	0.1368	-0.2167	1.8063	-0.1308	1.2748	0.0021	-0.0914	-0.0658	0.212	-0.0153	-0.0989	-0.0441	0.042	0.0057	0.1654	0.0056	-0.0037	0.1177	0.0125	0.1257	-41.8834	-13.9131	-8.64
6	4.8069	-2.6905	-1.7414	3.841	2.1301	1.3568	0.3301	0.3343	0.2271	-0.3478	-0.2608	-0.1347	-0.2063	0.0987	-0.0582	0.2232	0.0351	0.0218	0.2203	0.0603	0.1688	-48.1651	-6.3056	-28.2881
7	1.4841	0.0409	1.1907	2.4264	-0.2228	2.007	0.0393	-0.0554	0.0758	0.0626	-0.0626	0.0906	-0.0212	-0.0378	0.0213	0.1366	0.0276	0.0289	0.1586	0.0157	0.1159	-51.372	-1.2912	-11.8681
8	5.8559	1.046	-1.9087	4.2911	-3.1667	8.0775	-0.1046	-0.1442	0.4889	0.3206	-0.033	0.4318	-0.2129	-0.4455	0.0752	0.1915	0.0407	0.033	0.1384	-0.0628	0.2217	-51.7665	10.7963	-6.1512
9	3.1954	1.9987	-1.2632	2.0514	-0.8633	2.1299	-0.0437	0.6083	0.381	-0.0017	0.2462	-0.0776	-0.4263	0.1424	-0.1657	0.2522	-0.0764	0.0196	0.2743	0.0352	0.2362	-29.8053	13.5544	-11.7287
10	3.8009	0.2682	0.3945	3.4856	-0.8591	0.7842	-0.0276	0.436	0.6637	-0.0673	-0.025	-0.0392	-0.2444	0.0489	0.04	0.2213	-0.0432	-0.0125	0.198	0.0296	0.1863	-33.3518	15.8714	-8.6264
11	5.7564	-0.1954	-2.0609	3.787	1.0196	1.7757	0.0658	0.1528	-0.0605	0.1757	0.0558	-0.2032	0.0134	0.03	-0.0874	0.1734	-0.0126	-0.0298	0.1292	0.016	0.1548	-28.4909	2.851	-6.1729

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 304 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 25 through 67 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 68 through 118 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 119 through 136 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 137 through 200 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 201 through 221 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 222 through 246 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 247 through 284 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 285 through 304 )

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