PDB-5fff: Noroxomaritidine/Norcraugsodine Reductase in complex with NADP+ a...

ID or keywords:

Entry

Database: PDB / ID: 5fff

Title

Noroxomaritidine/Norcraugsodine Reductase in complex with NADP+ and piperonal

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: 1.501 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5fff.cif.gz	225.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5fff.ent.gz	180 KB	Display	PDB format
PDBx/mmJSON format	5fff.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5fff_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5fff_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5fff_validation.xml.gz	28.1 KB	Display
Data in CIF	5fff_validation.cif.gz	42.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ff/5fff ftp://data.pdbj.org/pub/pdb/validation_reports/ff/5fff	HTTPS FTP

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Related structure data

Related structure data	5feuSC 5ff9C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6y4d-1 5mtp-1 4egf-1 3gaf-1 5u9p-d 5ff9-d 5ugt-d 4lvu-1 4amw-2 6f9q-d Search similar-shape structures by Omokage search (details) 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

hetero molecules

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

1

A: Noroxomaritidine/Norcraugsodine Reductase

B: Noroxomaritidine/Norcraugsodine Reductase

hetero molecules

A: Noroxomaritidine/Norcraugsodine Reductase

B: Noroxomaritidine/Norcraugsodine Reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.386, 73.386, 167.892
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Noroxomaritidine/Norcraugsodine Reductase Mass: 27634.318 Da / Num. of mol.: 2 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.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-5XC / 1,3-benzodioxole-5-carbaldehyde Mass: 150.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₆O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 653 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.91 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 35% MPD, 100 mM sodium acetate (pH 4.5)

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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: Jul 9, 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: 1.501→35.85 Å / Num. obs: 84466 / % possible obs: 99.9 % / Redundancy: 10.2 % / R_sym value: 0.071 / Net I/σ(I): 17.6
Reflection shell	Resolution: 1.5→1.55 Å / Redundancy: 1.4 % / R_merge(I) obs: 0.071 / Mean I/σ(I) obs: 2.3 / % possible all: 98.7

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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
PDB_EXTRACT	3.15	data extraction
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FEU

5feu

Resolution: 1.501→35.847 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1657	4290	5.08 %
R_work	0.1499	-	-
obs	0.1508	84466	99.86 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.501→35.847 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3870	0	107	653	4630

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4181
X-RAY DIFFRACTION	f_angle_d	0.969	5722
X-RAY DIFFRACTION	f_dihedral_angle_d	16.447	2540
X-RAY DIFFRACTION	f_chiral_restr	0.058	662
X-RAY DIFFRACTION	f_plane_restr	0.005	731

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 (%)
1.5005-1.5176	0.2262	124	0.2161	2524	X-RAY DIFFRACTION	96
1.5176-1.5354	0.2123	149	0.2049	2633	X-RAY DIFFRACTION	100
1.5354-1.5542	0.2095	143	0.1911	2669	X-RAY DIFFRACTION	100
1.5542-1.5738	0.2127	157	0.1799	2591	X-RAY DIFFRACTION	100
1.5738-1.5946	0.1776	144	0.1624	2703	X-RAY DIFFRACTION	100
1.5946-1.6164	0.1893	142	0.1653	2582	X-RAY DIFFRACTION	100
1.6164-1.6395	0.1661	113	0.1617	2673	X-RAY DIFFRACTION	100
1.6395-1.664	0.1641	161	0.1567	2646	X-RAY DIFFRACTION	100
1.664-1.69	0.2229	131	0.1714	2627	X-RAY DIFFRACTION	100
1.69-1.7177	0.2004	148	0.1748	2675	X-RAY DIFFRACTION	100
1.7177-1.7473	0.2022	144	0.1658	2664	X-RAY DIFFRACTION	100
1.7473-1.7791	0.207	127	0.1616	2647	X-RAY DIFFRACTION	100
1.7791-1.8133	0.2001	146	0.1597	2657	X-RAY DIFFRACTION	100
1.8133-1.8503	0.1823	148	0.1508	2634	X-RAY DIFFRACTION	100
1.8503-1.8905	0.1859	135	0.1512	2667	X-RAY DIFFRACTION	100
1.8905-1.9345	0.1922	135	0.1504	2665	X-RAY DIFFRACTION	100
1.9345-1.9829	0.172	177	0.1581	2633	X-RAY DIFFRACTION	100
1.9829-2.0365	0.1768	154	0.1543	2652	X-RAY DIFFRACTION	100
2.0365-2.0964	0.1762	118	0.1527	2686	X-RAY DIFFRACTION	100
2.0964-2.1641	0.1649	116	0.1464	2692	X-RAY DIFFRACTION	100
2.1641-2.2414	0.1516	146	0.1462	2682	X-RAY DIFFRACTION	100
2.2414-2.3311	0.1663	151	0.1445	2648	X-RAY DIFFRACTION	100
2.3311-2.4372	0.1547	166	0.1401	2675	X-RAY DIFFRACTION	100
2.4372-2.5656	0.1399	132	0.1437	2702	X-RAY DIFFRACTION	100
2.5656-2.7263	0.1538	131	0.1498	2729	X-RAY DIFFRACTION	100
2.7263-2.9367	0.1694	160	0.1487	2705	X-RAY DIFFRACTION	100
2.9367-3.2321	0.1367	131	0.1481	2706	X-RAY DIFFRACTION	100
3.2321-3.6994	0.1494	165	0.1351	2710	X-RAY DIFFRACTION	100
3.6994-4.6592	0.1542	134	0.133	2795	X-RAY DIFFRACTION	100
4.6592-35.8571	0.1566	162	0.1512	2904	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	0.9937	-1.3384	0.8574	3.3463	-1.6213	1.5544	0.1039	0.1141	-0.1056	-0.0974	-0.0053	0.2386	0.024	0.051	-0.1078	0.1203	-0.0212	-0.0149	0.1381	-0.0354	0.1288	8.5877	69.5595	10.6148
2	2.9772	-0.1171	1.019	2.4418	-1.0024	3.3329	0.0002	0.0836	-0.4167	-0.1168	0.0524	0.2967	0.3743	-0.3099	-0.0546	0.1892	-0.0294	0.0121	0.1503	-0.0696	0.2248	12.1923	55.4813	14.4334
3	6.6443	-2.231	5.9421	2.3277	-1.964	6.6242	0.1104	0.5705	-0.509	-0.2463	-0.0043	-0.1517	0.4435	0.3454	-0.0783	0.165	-0.0051	0.0319	0.1886	-0.0858	0.2333	26.5463	57.5912	10.8084
4	0.6861	0.2724	0.0356	0.6665	0.0364	0.7009	0.0038	0.042	-0.0627	0.0011	-0.0065	-0.0203	0.0488	0.0024	0.0057	0.1189	0.0003	-0.0073	0.1243	-0.007	0.1248	24.4141	70.4252	22.6828
5	1.1192	0.3564	-0.5563	0.9461	-0.4252	1.504	0.0084	-0.0013	-0.0829	0.0246	-0.0269	0.0176	0.0664	0.0286	-0.0116	0.122	-0.001	-0.0194	0.1161	-0.0145	0.1327	15.0955	71.3257	23.6283
6	1.4015	0.5547	-1.2305	1.1099	-0.7352	3.5674	0.0157	-0.0754	-0.0207	0.1293	-0.0403	0.0149	0.0132	-0.0078	0.0289	0.0976	0.0145	-0.0122	0.0846	-0.0006	0.1153	9.7649	77.7868	26.682
7	1.0487	-2.1989	0.3293	4.8951	-0.2405	0.8115	0.1122	0.1124	-0.1124	-0.1603	-0.1344	0.4177	0.0383	-0.0139	0.0029	0.09	-0.001	-0.0316	0.1653	-0.016	0.12	-2.0063	86.6223	11.445
8	2.2618	0.8703	0.4718	3.9443	1.0579	3.6305	-0.0615	0.5223	0.2315	-0.6051	-0.0184	0.3779	-0.2085	-0.1489	0.0782	0.1651	0.0366	-0.0476	0.2696	0.0506	0.2022	-6.3281	100.2813	7.0002
9	7.5643	6.635	2.9721	7.971	2.878	1.7998	0.0281	-0.206	0.4914	0.0375	-0.1251	0.7177	-0.1139	-0.3107	0.076	0.1394	0.0327	0.0086	0.1662	0.0253	0.2369	-9.4157	104.6248	21.1284
10	1.3078	0.4688	-0.0027	0.8266	-0.221	0.481	0.0101	0.0571	0.0769	0.0197	0.0062	0.0753	-0.0328	-0.0288	-0.0187	0.0954	0.0043	0.0082	0.1001	0.0048	0.0983	6.9924	98.7268	22.9146
11	1.9363	1.2055	-1.3617	1.6888	-1.145	1.7032	-0.0143	0.118	0.0234	-0.0298	-0.0084	-0.0429	-0.0731	0.0259	0.0453	0.1154	0.0011	-0.0167	0.1089	0.0019	0.0909	15.7499	91.5763	11.1956

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 48 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 85 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 86 through 99 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 100 through 192 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 193 through 219 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 220 through 271 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 15 through 48 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 49 through 85 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 86 through 99 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 100 through 205 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 206 through 271 )

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