PDB-9cv8: Crystal Structure of Cytochrome P450 NysL bound to nystatin

ID or keywords:

Entry

Database: PDB / ID: 9cv8

Title

Crystal Structure of Cytochrome P450 NysL bound to nystatin

Components

NysL

Keywords

OXIDOREDUCTASE / Cytochrome P450 / Nystatin / Macrolide

Function / homology

Function and homology information

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function

Biological species

Streptomyces noursei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Murarka, V.C. / Poulos, T.L.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2025
Title: Crystal structure of cytochrome P450 NysL and the structural basis for stereo- and regio-selective oxidation of antifungal macrolides.
Authors: Murarka, V.C. / Kim, J.S. / Lamb, D.C. / Kelly, S.L. / Poulos, T.L. / Follmer, A.H.

History

Deposition	Jul 28, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 29, 2025	Provider: repository / Type: Initial release
Revision 1.1	Feb 26, 2025	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9cv8.cif.gz	340.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cv/9cv8 ftp://data.pdbj.org/pub/pdb/validation_reports/cv/9cv8	HTTPS FTP

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Related structure data

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	#82 - Oct 2006 Cytochrome p450 similarity (2)

Deposited unit

A: NysL

B: NysL

hetero molecules

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

1

A: NysL

hetero molecules

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

2

B: NysL

hetero molecules

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

Unit cell

Length a, b, c (Å)	136.290, 136.290, 135.600
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	NysL Mass: 43170.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces noursei (bacteria) / Gene: nysL / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L4X0
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-A1AZ7 / Nystatin / (1S,3R,4R,7R,9R,11R,15S,16R,17R,18S,19E,21E,25E,27E,29E,31E,33R,35S,36R,37S)-33-[(3-amino-3,6-dideoxy-beta-D-mannopyranosyl)oxy]-1,3,4,7,9,11,17,37-octahydroxy-15,16,18-trimethyl-13-oxo-14,39-dioxabicyclo[33.3.1]nonatriaconta-19,21,25,27,29,31-hexaene-36-carboxylic acid Mass: 926.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄₇H₇₅NO₁₇ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 535 / 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: 4.1 Å³/Da / Density % sol: 70 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 100 mM Bis-tris propane (pH 7), 1.5 M lithium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2021
Radiation	Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2→37.79 Å / Num. obs: 98254 / % possible obs: 99.76 % / Redundancy: 9.1 % / CC_1/2: 0.995 / R_merge(I) obs: 0.1727 / R_pim(I) all: 0.05345 / R_rim(I) all: 0.1809 / Χ²: 0.86 / Net I/σ(I): 18.25
Reflection shell	Resolution: 2→2.072 Å / Redundancy: 2.1 % / R_merge(I) obs: 1.03 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 9674 / CC_1/2: 0.906 / CC star: 0.975 / R_pim(I) all: 0.3196 / R_rim(I) all: 1 / Χ²: 0.57

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Processing

Software

Name	Version	Classification
PHENIX	v1.18-3845-000	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→37.79 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2153	4712	4.81 %
R_work	0.1888	-	-
obs	0.1901	98060	99.78 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→37.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6017	0	261	535	6813

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6542
X-RAY DIFFRACTION	f_angle_d	1.057	8972
X-RAY DIFFRACTION	f_dihedral_angle_d	13.622	2416
X-RAY DIFFRACTION	f_chiral_restr	0.126	1039
X-RAY DIFFRACTION	f_plane_restr	0.005	1159

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 (%)
2-2.02	0.3104	156	0.2914	3059	X-RAY DIFFRACTION	99
2.02-2.05	0.2848	149	0.2855	3062	X-RAY DIFFRACTION	99
2.05-2.07	0.28	150	0.2818	3098	X-RAY DIFFRACTION	99
2.07-2.1	0.2862	141	0.2746	3055	X-RAY DIFFRACTION	100
2.1-2.13	0.2622	148	0.2618	3101	X-RAY DIFFRACTION	100
2.13-2.15	0.2751	169	0.2433	3054	X-RAY DIFFRACTION	100
2.15-2.19	0.262	159	0.2426	3110	X-RAY DIFFRACTION	100
2.19-2.22	0.2612	159	0.2276	3039	X-RAY DIFFRACTION	100
2.22-2.25	0.2521	136	0.223	3112	X-RAY DIFFRACTION	100
2.25-2.29	0.2485	150	0.2235	3092	X-RAY DIFFRACTION	100
2.29-2.33	0.2351	168	0.2124	3089	X-RAY DIFFRACTION	100
2.33-2.37	0.2518	132	0.2097	3090	X-RAY DIFFRACTION	100
2.37-2.42	0.2363	143	0.2167	3085	X-RAY DIFFRACTION	100
2.42-2.47	0.2454	154	0.2132	3134	X-RAY DIFFRACTION	100
2.47-2.52	0.2489	167	0.2155	3087	X-RAY DIFFRACTION	100
2.52-2.58	0.2287	146	0.209	3090	X-RAY DIFFRACTION	100
2.58-2.64	0.2908	205	0.2208	3073	X-RAY DIFFRACTION	100
2.64-2.71	0.2629	141	0.2183	3142	X-RAY DIFFRACTION	100
2.71-2.79	0.2472	150	0.2132	3090	X-RAY DIFFRACTION	100
2.79-2.88	0.2259	169	0.2132	3094	X-RAY DIFFRACTION	100
2.88-2.99	0.247	160	0.2185	3131	X-RAY DIFFRACTION	100
2.99-3.11	0.2625	165	0.2176	3129	X-RAY DIFFRACTION	100
3.11-3.25	0.1909	166	0.1992	3097	X-RAY DIFFRACTION	100
3.25-3.42	0.209	203	0.179	3082	X-RAY DIFFRACTION	100
3.42-3.63	0.1862	159	0.1624	3129	X-RAY DIFFRACTION	100
3.63-3.91	0.2	159	0.1549	3153	X-RAY DIFFRACTION	100
3.91-4.31	0.1669	148	0.1461	3156	X-RAY DIFFRACTION	100
4.31-4.93	0.1603	170	0.1367	3168	X-RAY DIFFRACTION	100
4.93-6.21	0.1844	152	0.1716	3231	X-RAY DIFFRACTION	100
6.21-37.79	0.2003	138	0.1689	3316	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	7.507	3.9571	-5.6364	2.6186	-1.8759	6.6437	0.0472	-0.8792	-0.0569	0.3898	-0.251	-0.4986	-0.681	1.2477	0.1774	0.6869	-0.2077	-0.0733	0.5845	-0.0672	0.4064	77.556	-13.1363	-24.4935
2	0.5321	-0.0891	0.2195	0.7714	-0.3559	2.4369	0.0482	0.102	0.1003	-0.0026	0.0331	-0.028	-0.394	0.0058	-0.0841	0.3373	0.0194	0.0144	0.1746	-0.0363	0.2486	64.2533	-21.4779	-40.1261
3	0.1513	0.1531	-0.1757	0.3058	0.273	4.1554	0.0097	-0.0207	-0.1339	0.0237	-0.0231	-0.05	0.4327	0.0068	0.0114	0.2895	0.01	-0.0165	0.2383	0.0129	0.3018	62.0435	-40.0434	-36.9829
4	0.6896	0.0619	-0.3521	0.613	-0.5859	2.6268	0.0805	-0.0524	0.1154	0.1807	0.0238	-0.0047	-0.6847	-0.0237	-0.0891	0.3782	0.017	0.0234	0.1859	-0.0137	0.2433	62.2371	-21.462	-25.7613
5	7.599	2.7927	-6.6089	3.7893	0.4237	9.2386	0.3076	0.5167	1.2254	0.776	0.3939	0.5228	-1.3172	-0.8611	-0.7276	0.7344	0.1044	0.0849	0.3128	0.0458	0.6184	54.2368	20.451	-53.7002
6	0.6052	0.0778	-0.0895	1.9152	-0.996	3.7586	-0.0755	-0.0204	-0.0115	0.2287	0.1522	0.2632	0.3174	-0.4108	-0.0857	0.4141	0.0129	0.0592	0.2799	0.0402	0.369	52.3391	-1.0101	-59.9072
7	1.5137	0.3551	-0.6106	4.8288	-0.8395	2.8707	-0.1201	0.0599	-0.0783	-0.2678	0.2198	0.7867	0.3493	-0.8039	-0.0878	0.3969	-0.0728	-0.0358	0.4657	0.0707	0.4208	43.7828	-1.8744	-76.3203
8	0.9003	0.3786	-0.6768	2.0389	-1.4371	3.6958	-0.0398	-0.0125	0.0822	0.1635	-0.0003	0.0394	-0.1949	-0.0789	0.041	0.3848	0.0362	0.0235	0.1829	0.0254	0.2996	59.5503	9.5476	-66.7847

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 6 through 30 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 31 through 130 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 131 through 218 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 219 through 394 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 5 through 30 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 31 through 130 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 131 through 218 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 219 through 394 )

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