PDB-7n79: O2-, PLP-dependent desaturase Plu4 holo-enzyme

ID or keywords:

Entry

Database: PDB / ID: 7n79

Title

O2-, PLP-dependent desaturase Plu4 holo-enzyme

Components

Aminotran_1_2 domain-containing protein

Keywords

BIOSYNTHETIC PROTEIN / arginine desaturase / oxygen- and PLP-dependent oxidase / Fold Type I / biosynthesis

Function / homology

Function and homology information

amino acid metabolic process / transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function

Biological species

Pseudoalteromonas luteoviolacea (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.98 Å

Authors

Hoffarth, E.R. / Ryan, K.S.

Funding support

Canada, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: A shared mechanistic pathway for pyridoxal phosphate-dependent arginine oxidases.
Authors: Hoffarth, E.R. / Caddell Haatveit, K. / Kuatsjah, E. / MacNeil, G.A. / Saroya, S. / Walsby, C.J. / Eltis, L.D. / Houk, K.N. / Garcia-Borras, M. / Ryan, K.S.

History

Deposition	Jun 9, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 6, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7n79.cif.gz	328.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7n79.ent.gz	265.2 KB	Display	PDB format
PDBx/mmJSON format	7n79.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7n79_validation.pdf.gz	484.1 KB	Display	wwPDB validaton report
Full document	7n79_full_validation.pdf.gz	495.8 KB	Display
Data in XML	7n79_validation.xml.gz	34 KB	Display
Data in CIF	7n79_validation.cif.gz	47.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n7/7n79 ftp://data.pdbj.org/pub/pdb/validation_reports/n7/7n79	HTTPS FTP

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Related structure data

Related structure data	7rf9C 7rgbC 6c3dS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7rf9-2 6c92-1 3qgu-d 5luc-3 7rf9-1 7rgb-2 6c92-2 5dj3-1 6c3a-d 2hui-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

Deposited unit

A: Aminotran_1_2 domain-containing protein

B: Aminotran_1_2 domain-containing protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, homology

Unit cell

Length a, b, c (Å)	75.022, 72.195, 76.271
Angle α, β, γ (deg.)	90.000, 112.090, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Aminotran_1_2 domain-containing protein / Oxygen- / PLP-dependent L-arginine desaturase Mass: 44867.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas luteoviolacea (bacteria) Gene: JF50_03865 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C1MLE8
#2: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.13 Å³/Da / Density % sol: 42.33 % / Description: plates
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris:HCl; 27% PEG 3350; 0.2 M ammonium acetate; microseeded from crystals grown at pH 6.0; soaked with 2 mM PLP for 2 h Temp details: room temperature

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97946 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97946 Å / Relative weight: 1

Reflection

Resolution: 1.98→37.75 Å / Num. obs: 52155 / % possible obs: 98.6 % / Redundancy: 6.9 % / CC_1/2: 0.997 / R_merge(I) obs: 0.07 / R_pim(I) all: 0.029 / R_rim(I) all: 0.076 / Net I/σ(I): 15.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.98-2.03	6.6	2.012	23147	3510	0.514	0.838	2.185	1.4	94.2
9.06-37.75	7.2	0.051	4209	588	0.998	0.02	0.055	48	99

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6C3D

6c3d

Resolution: 1.98→37.75 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2152	2642	5.07 %
R_work	0.166	49478	-
obs	0.1684	52120	98.44 %

Solvent computation

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

Displacement parameters

B_iso max: 121.3 Å² / B_iso mean: 51.4718 Å² / B_iso min: 25.75 Å²

Refinement step

Cycle: final / Resolution: 1.98→37.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6004	0	52	330	6386
B_iso mean	-	-	79.53	51.69	-
Num. residues	-	-	-	-	756

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.98-2.0129	0.3235	113	0.2934	2471	92
2.0129-2.0516	0.3182	135	0.2556	2590	100
2.0516-2.0935	0.3223	160	0.2471	2601	99
2.0935-2.139	0.2932	158	0.2276	2597	99
2.139-2.1887	0.289	146	0.2223	2604	99
2.1887-2.2435	0.2675	142	0.2136	2605	99
2.2435-2.3041	0.2526	147	0.2083	2454	95
2.3041-2.3719	0.2522	155	0.194	2592	98
2.3719-2.4485	0.2459	105	0.1851	2637	100
2.4485-2.5359	0.2364	137	0.1834	2639	100
2.5359-2.6375	0.2594	149	0.1903	2643	100
2.6375-2.7575	0.2635	132	0.1871	2619	99
2.7575-2.9028	0.2693	141	0.1864	2609	99
2.9028-3.0846	0.2472	130	0.1812	2563	97
3.0846-3.3226	0.2428	146	0.1765	2616	99
3.3226-3.6567	0.1914	155	0.1603	2628	99
3.6567-4.1853	0.1933	125	0.1353	2666	99
4.1853-5.2707	0.1356	119	0.1277	2655	99
5.2707-37.75	0.1865	147	0.1488	2689	99

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	1.6546	-1.2286	-0.4279	5.2425	-0.2177	1.8962	0.035	-0.1739	0.058	-0.2568	-0.0488	0.3439	-0.121	-0.4757	0.143	0.3119	-0.0401	0.0652	0.6443	-0.0961	0.44	18.0662	30.7703	55.0953
2	2.5278	0.2491	-0.1034	3.5482	-0.1533	0.8123	0.224	-0.7906	0.372	0.5859	-0.1415	-0.3839	-0.1913	0.1249	-0.3232	0.3971	-0.0574	-0.0695	0.4801	-0.1091	0.3667	42.7951	38.295	63.054
3	2.4967	0.0797	0.2106	3.063	-0.1351	4.0891	0.0924	-0.7803	-0.5167	0.4411	-0.1325	-0.5797	-0.1494	0.1983	-0.3206	0.3117	-0.0591	-0.0762	0.4437	0.1379	0.3378	41.1296	19.2483	58.9934
4	3.7388	0.5082	-0.0949	4.5602	0.0007	2.2052	-0.0273	-0.474	-0.4838	-0.0065	-0.0955	-0.1026	0.4785	-0.2208	-0.1379	0.3295	-0.0895	-0.0056	0.3166	0.0851	0.3417	29.5712	9.6551	53.1096
5	0.7065	-1.0417	-1.144	1.8062	1.2657	2.5289	0.1615	-1.3139	-0.7549	0.724	-0.1593	0.1836	0.4866	-0.2588	-0.4286	0.6222	-0.2659	-0.0116	0.8377	0.2314	0.608	25.4397	3.3173	67.6553
6	2.4396	0.0477	0.4658	0.6738	-1.0479	1.7941	0.2635	-1.0594	-0.5737	0.58	-0.4525	-0.1998	0.4749	-0.3239	-0.5729	0.5031	-0.1797	-0.0729	0.7068	0.2827	0.4691	28.133	10.0821	65.3009
7	1.236	-0.181	1.0682	3.0411	-2.2467	2.5971	0.332	-1.6242	-0.6589	0.8792	-0.527	-0.4879	0.3264	-0.3112	-0.9378	0.6738	-0.3193	-0.1826	0.8707	0.4469	0.49	33.5509	12.7237	70.5158
8	2.109	0.5113	-0.4676	4.4485	-0.2328	2.3207	0.1688	-0.7524	-0.3059	0.4771	-0.3922	-0.4154	0.1578	0.0814	-0.5114	0.3543	-0.1083	-0.069	0.5248	0.1264	0.3107	37.5518	21.3417	63.3234
9	1.6162	0.495	-0.2923	2.466	0.1233	2.0667	0.1683	-0.6622	0.042	0.2705	-0.2337	-0.1204	-0.1809	-0.0463	-0.3439	0.2771	-0.0593	-0.0661	0.4074	0.0016	0.2486	40.1117	29.8197	60.4063
10	2.5262	0.0231	-0.4754	3.6557	0.5805	1.8642	0.1969	-0.59	-0.0533	0.4058	-0.2882	0.4869	0.0766	-0.5761	-0.1063	0.382	-0.1249	0.0721	0.7476	-0.0675	0.395	11.322	22.6156	62.8513
11	8.4416	3.113	1.7916	6.9306	1.1469	2.3702	0.1172	-0.891	0.0192	0.089	-0.3274	0.6605	-0.2936	-0.7312	0.1552	0.4442	0.0631	0.0907	0.7966	-0.137	0.5807	3.2574	33.0247	61.7445
12	2.9639	-0.2686	0.466	5.012	0.3018	2.6672	-0.0288	-0.2611	-0.1419	-0.0897	0.1546	-0.1046	0.0327	0.2314	-0.0638	0.2698	-0.0368	0.0622	0.3259	0.0539	0.4077	53.2996	33.6188	46.7141
13	1.8414	-0.141	-0.3586	0.757	0.6736	1.4459	0.0022	-0.0594	0.5809	-0.1061	-0.0866	0.224	-0.4236	-0.3608	0.0091	0.3899	0.0921	-0.0387	0.3443	-0.0281	0.4944	28.693	44.8105	46.2207
14	2.9525	0.2279	-0.7638	5.4914	0.5162	2.3548	-0.0588	0.4678	0.3327	-0.2962	-0.0005	0.4724	-0.0793	-0.3496	0.1312	0.2497	0.0087	-0.0478	0.3011	0.0078	0.2677	30.4089	28.438	35.8961
15	1.7996	0.4722	-0.9133	0.6477	-0.7078	3.2138	-0.1382	0.4468	-0.5563	-0.6293	0.0577	-0.3204	0.3402	-0.0163	-0.1729	0.4713	-0.0132	0.0942	0.2315	-0.0703	0.3994	42.1071	16.7112	34.5842
16	2.4623	0.1724	2.0155	5.0742	0.0786	4.5843	0.1708	1.2322	-0.3097	-0.7718	0.0378	-0.0639	0.1452	0.1931	-0.6033	0.7498	0.0665	0.1866	0.62	-0.1467	0.5234	45.5218	20.6239	18.8384
17	3.8366	0.4262	0.1917	2.2941	0.1305	2.5561	0.025	0.7271	-0.0202	-0.5172	-0.0359	-0.1681	0.0262	-0.2433	-0.1894	0.5165	0.0411	0.0587	0.4477	0.0041	0.3215	39.9595	28.587	24.2851
18	2.8118	1.0118	0.0867	1.5826	1.0175	2.7459	0.118	0.3269	0.2846	-0.3256	-0.0762	0.1129	0.0011	-0.4084	-0.028	0.3979	0.0674	-0.0455	0.3088	0.0425	0.317	34.8021	32.7652	34.7241
19	2.786	0.7024	-0.2265	4.7599	0.4933	2.3265	0.0141	0.0746	0.4851	-0.0681	-0.091	0.4733	-0.1077	-0.2783	0.0164	0.2135	0.0683	-0.0615	0.2804	-0.0079	0.3278	29.2625	33.9501	42.2482
20	5.6971	-1.9688	0.4229	4.407	0.38	1.265	-0.3009	0.3249	1.6169	-0.4667	0.1794	-0.614	-0.5032	0.0876	0.1274	0.5458	-0.0181	0.0557	0.2685	0.101	0.6601	54.618	46.3407	34.8598
21	4.0553	0.0637	0.2183	2.4916	0.1247	2.0598	0.0688	0.3815	-0.2482	-0.3425	-0.0597	-0.6524	-0.1466	0.3136	0.0371	0.3707	-0.0151	0.1514	0.3332	0.0501	0.7384	63.4216	31.8219	34.3903
22	2.2417	1.3709	0.5711	5.316	2.4577	2.6954	0.1696	0.0571	-0.1032	-0.2614	-0.0011	-0.8064	0.0193	0.2336	-0.2327	0.3325	0.022	0.1256	0.2436	0.0572	0.4886	57.9932	26.3519	37.0907
23	4.5699	-3.0063	-0.3361	6.442	1.5481	3.0126	0.161	-0.1648	0.0444	-0.0597	0.023	-0.7954	-0.0482	0.5689	-0.077	0.3958	-0.0745	0.008	0.4094	0.0126	0.6593	67.9345	39.8736	43.5659

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 36 )	A	5 - 36
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 70 )	A	37 - 70
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 71 through 100 )	A	71 - 100
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 101 through 125 )	A	101 - 125
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 126 through 144 )	A	126 - 144
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 145 through 166 )	A	145 - 166
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 167 through 199 )	A	167 - 199
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 200 through 237 )	A	200 - 237
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 238 through 275 )	A	238 - 275
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 276 through 360 )	A	276 - 360
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 361 through 381 )	A	361 - 381
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 5 through 36 )	B	5 - 36
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 37 through 69 )	B	37 - 69
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 70 through 100 )	B	70 - 100
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 101 through 125 )	B	101 - 125
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 126 through 146 )	B	126 - 146
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 147 through 199 )	B	147 - 199
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 200 through 234 )	B	200 - 234
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 235 through 270 )	B	235 - 270
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 271 through 291 )	B	271 - 291
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 292 through 331 )	B	292 - 331
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 332 through 360 )	B	332 - 360
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 361 through 381 )	B	361 - 381

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