PDB-5ff9: Noroxomaritidine/Norcraugsodine Reductase in Complex with NADP+ a...

ID or keywords:

Entry

Database: PDB / ID: 5ff9

Title

Noroxomaritidine/Norcraugsodine Reductase in Complex with NADP+ and tyramine

Components

Noroxomaritidine/Norcraugsodine Reductase

Keywords

OXIDOREDUCTASE / short-chain dehydrogenase/reductase alkaloid biosynthesis

Function / homology

Function and homology information

alkaloid metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleotide binding
Similarity search - Function

Biological species

Narcissus pseudonarcissus (daffodil)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.814 Å

Authors

Jez, J.M. / Holland, C.K.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: Identification of a Noroxomaritidine Reductase with Amaryllidaceae Alkaloid Biosynthesis Related Activities.
Authors: Kilgore, M.B. / Holland, C.K. / Jez, J.M. / Kutchan, T.M.

History

Deposition	Dec 18, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 8, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 15, 2016	Group: Database references
Revision 1.2	Aug 17, 2016	Group: Database references
Revision 1.3	Sep 20, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ff9.cif.gz	402.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5ff9.ent.gz	331 KB	Display	PDB format
PDBx/mmJSON format	5ff9.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/ff/5ff9 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/5ff9	HTTPS FTP

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Related structure data

Related structure data	5feuC 5fffC 2ae2S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3gr6-d 5tii-2 4d42-1 4bgi-1 4bgi-3 6tbb-2 5ycr-d 4bge-1 5fff-1 5er6-d Search similar-shape structures by Omokage search (details) 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	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: Noroxomaritidine/Norcraugsodine Reductase

B: Noroxomaritidine/Norcraugsodine Reductase

C: Noroxomaritidine/Norcraugsodine Reductase

D: Noroxomaritidine/Norcraugsodine Reductase

hetero molecules

114 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	61.800, 86.964, 186.115
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Noroxomaritidine/Norcraugsodine Reductase Mass: 27634.318 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Narcissus pseudonarcissus (daffodil) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1A9TAK5*PLUS
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-AEF / 4-(2-aminoethyl)phenol Mass: 137.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₁NO
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.63 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 2 M ammonium sulfate, 100 mM CAPS buffer (pH 10.5), 200 mM lithium sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.81→39.4 Å / Num. obs: 90846 / % possible obs: 99.2 % / Redundancy: 10.4 % / R_sym value: 0.098 / Net I/σ(I): 23.7
Reflection shell	Resolution: 1.81→1.88 Å / Redundancy: 11 % / R_merge(I) obs: 0.574 / Mean I/σ(I) obs: 2.3 / % possible all: 91.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-3000		data collection
SCALEPACK		data scaling
PHASER		phasing
PDB_EXTRACT	3.15	data extraction
HKL-3000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2AE2

2ae2

Resolution: 1.814→39.394 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2139	4546	5 %
R_work	0.1844	-	-
obs	0.1859	90846	99.16 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.814→39.394 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7540	0	194	445	8179

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7958
X-RAY DIFFRACTION	f_angle_d	1.009	10840
X-RAY DIFFRACTION	f_dihedral_angle_d	16.223	4754
X-RAY DIFFRACTION	f_chiral_restr	0.059	1243
X-RAY DIFFRACTION	f_plane_restr	0.006	1386

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 (%)
1.8139-1.8345	0.2546	120	0.2372	2106	X-RAY DIFFRACTION	75
1.8345-1.8561	0.3201	152	0.2499	2842	X-RAY DIFFRACTION	100
1.8561-1.8787	0.2807	137	0.2329	2906	X-RAY DIFFRACTION	100
1.8787-1.9025	0.2664	154	0.2261	2852	X-RAY DIFFRACTION	100
1.9025-1.9276	0.2677	143	0.2276	2885	X-RAY DIFFRACTION	100
1.9276-1.954	0.2479	146	0.2163	2849	X-RAY DIFFRACTION	100
1.954-1.9819	0.2338	152	0.2091	2896	X-RAY DIFFRACTION	100
1.9819-2.0115	0.2506	155	0.2106	2838	X-RAY DIFFRACTION	100
2.0115-2.0429	0.2297	150	0.1989	2862	X-RAY DIFFRACTION	100
2.0429-2.0764	0.2196	155	0.1949	2883	X-RAY DIFFRACTION	100
2.0764-2.1122	0.2136	139	0.1927	2894	X-RAY DIFFRACTION	100
2.1122-2.1506	0.2446	142	0.1904	2869	X-RAY DIFFRACTION	100
2.1506-2.1919	0.2415	157	0.1922	2878	X-RAY DIFFRACTION	100
2.1919-2.2367	0.2518	163	0.1981	2869	X-RAY DIFFRACTION	100
2.2367-2.2853	0.2367	151	0.1911	2913	X-RAY DIFFRACTION	100
2.2853-2.3385	0.2344	139	0.1844	2851	X-RAY DIFFRACTION	100
2.3385-2.3969	0.2276	135	0.1844	2920	X-RAY DIFFRACTION	100
2.3969-2.4617	0.2135	153	0.1837	2882	X-RAY DIFFRACTION	100
2.4617-2.5342	0.2323	134	0.1897	2912	X-RAY DIFFRACTION	100
2.5342-2.6159	0.2289	164	0.1856	2895	X-RAY DIFFRACTION	100
2.6159-2.7094	0.2232	130	0.1905	2923	X-RAY DIFFRACTION	100
2.7094-2.8179	0.1942	171	0.1932	2901	X-RAY DIFFRACTION	100
2.8179-2.9461	0.2565	160	0.191	2904	X-RAY DIFFRACTION	100
2.9461-3.1013	0.2178	164	0.1841	2895	X-RAY DIFFRACTION	100
3.1013-3.2956	0.2225	162	0.1865	2901	X-RAY DIFFRACTION	100
3.2956-3.5499	0.1721	152	0.1705	2941	X-RAY DIFFRACTION	100
3.5499-3.9068	0.1757	136	0.1645	2964	X-RAY DIFFRACTION	100
3.9068-4.4715	0.2107	172	0.1532	2965	X-RAY DIFFRACTION	100
4.4715-5.631	0.192	186	0.166	2983	X-RAY DIFFRACTION	100
5.631-39.403	0.1906	172	0.1954	3121	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	0.5459	-0.2016	0.4702	1.4806	-0.1573	0.7586	-0.2229	-0.0102	0.2104	0.2154	0.0645	0.1565	-0.4446	-0.0816	0.1903	0.5732	0.0629	0.1756	0.2503	0.1382	0.833	14.9351	25.0573	-9.7892
2	0.1386	0.1072	-0.0586	0.3126	-0.0428	0.1212	-0.0129	0.1286	0.3206	-0.0172	0.0875	0.1759	-0.2603	-0.1516	0.0912	0.4749	0.1232	0.1341	0.4531	0.3749	0.7791	16.0172	18.2893	-25.0348
3	1.2776	-0.582	0.3036	1.3957	0.0363	0.6023	-0.0116	0.063	0.1587	0.0964	0.0644	0.3568	-0.1672	-0.1652	-0.0204	0.3643	0.1194	0.1668	0.2522	0.1908	0.5394	13.153	7.7861	-13.9895
4	1.7579	-1.7162	0.1793	3.4536	-0.2418	1.4991	0.0621	-0.1724	0.5048	0.3488	-0.0222	-0.0364	-0.3653	0.0253	0.0197	0.3091	-0.0404	0.0767	0.1491	-0.049	0.294	25.8209	-2.1019	8.4793
5	2.7332	-0.1078	-0.9813	1.806	0.5598	3.713	0.1544	0.0226	0.135	0.0799	0.0018	0.0223	-0.0219	0.0682	-0.1332	0.1535	0.0047	0.007	0.0865	0.0133	0.1592	20.8457	-13.5341	-4.0506
6	1.9819	-0.2014	0.8999	1.7268	-0.1992	1.2125	0.1364	0.368	0.3497	-0.0809	-0.0952	-0.14	-0.1909	0.2205	-0.0482	0.2676	0.0397	0.0942	0.183	0.085	0.2994	27.4119	-0.7759	-10.2154
7	0.1451	0.0284	0.1338	0.7548	-0.469	0.7538	-0.0827	0.1257	0.0899	-0.3326	0.06	0.1095	-0.014	-0.2241	-0.0411	0.4545	-0.0117	-0.0309	1.1562	0.2736	0.391	12.7734	-8.4472	-52.9152
8	0.2497	-0.0432	0.2973	0.309	-0.0823	0.3579	-0.0441	0.3604	0.1627	-0.3092	0.1306	0.115	-0.0711	-0.1109	0.1768	0.5077	0.0421	0.0271	0.9857	0.4459	0.549	13.2583	3.4988	-48.3513
9	0.4827	0.0881	-0.2498	0.6803	-0.2426	2.0865	0.0236	0.2882	0.1701	-0.0913	0.0558	0.0377	-0.1091	0.1791	0.0937	0.3167	0.0471	0.0305	0.7177	0.2701	0.316	18.4838	-5.6406	-38.1165
10	0.7555	-0.1524	0.8545	1.9694	-0.2456	1.5559	-0.0463	0.4664	-0.1304	-0.3985	-0.0032	-0.0533	0.3087	-0.226	0.1528	0.3603	0.004	0.014	0.7619	-0.2534	0.3036	16.0621	-31.2615	-36.7611
11	0.3058	0.4477	0.5188	3.0554	-0.5043	1.5457	0.0447	0.5535	-0.3087	-0.3734	-0.0831	0.5469	0.6969	-0.5032	-0.0074	0.4492	-0.101	0.0114	0.8421	-0.4038	0.6722	12.2205	-41.5598	-31.1527
12	4.6438	-3.4894	-3.3554	7.7631	4.8187	3.6594	-0.209	0.4615	-0.9832	0.0426	0.2106	-0.2768	1.3014	0.2677	0.0016	0.4581	0.0056	0.0193	0.3515	-0.1749	0.52	26.1317	-39.2882	-23.5838
13	2.5341	-0.7961	-2.4524	1.9167	0.6688	3.9693	0.0207	0.442	-0.0945	-0.115	0.0917	-0.1241	0.1123	-0.0376	-0.1143	0.1547	-0.0023	-0.015	0.2917	-0.076	0.1801	18.7241	-25.3697	-20.9054
14	2.606	1.0272	-1.9748	1.0793	-0.9966	1.7017	-0.2376	0.6089	-0.1832	-0.1588	0.1917	-0.026	0.1557	-0.015	0.0552	0.2228	0.0427	0.0173	0.3681	-0.0246	0.1427	16.089	-21.3777	-23.9947
15	4.7474	-0.7915	-4.6688	1.1661	0.6386	5.3027	0.043	1.0181	0.1909	-0.078	0.1021	0.2508	-0.1702	-0.6834	-0.1498	0.2735	0.0109	-0.0234	0.7164	0.0536	0.2636	2.7472	-18.3519	-29.7502
16	2.8518	0.5659	-1.7312	1.2563	-0.6294	1.5789	0.0729	0.4819	0.132	-0.1075	0.0625	0.1034	-0.2155	-0.191	-0.1276	0.2545	0.0152	0.0053	0.6409	0.119	0.1984	14.8061	-12.914	-32.4615

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 16 through 72 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 73 through 192 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 193 through 271 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 15 through 85 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 86 through 192 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 193 through 271 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 18 through 58 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 59 through 172 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 173 through 270 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 17 through 58 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 59 through 85 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 86 through 99 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 100 through 172 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 173 through 219 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 220 through 249 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 250 through 271 )

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