PDB-5dj3: Structure of the PLP-Dependent L-Arginine Hydroxylase MppP with D...

ID or keywords:

Entry

Database: PDB / ID: 5dj3

Title

Structure of the PLP-Dependent L-Arginine Hydroxylase MppP with D-Arginine Bound

Components

PLP-Dependent L-Arginine Hydroxylase MppP

Keywords

TRANSFERASE /

aminotransferase /

hydroxylase /

enduracididine /

pyridoxal 5'-phosphate

Function / homology

Function and homology information

biosynthetic process /

pyridoxal phosphate binding
Similarity search - Function

Biological species

Streptomyces wadayamensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.227 Å

Authors

Silvaggi, N.R. / Han, L.

Citation

Journal: Biochemistry / Year: 2015
Title: Streptomyces wadayamensis MppP Is a Pyridoxal 5'-Phosphate-Dependent l-Arginine alpha-Deaminase, gamma-Hydroxylase in the Enduracididine Biosynthetic Pathway.
Authors: Han, L. / Schwabacher, A.W. / Moran, G.R. / Silvaggi, N.R.

History

Deposition	Sep 1, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 16, 2015	Group: Database references
Revision 1.2	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5dj3.cif.gz	786.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5dj3.ent.gz	669.2 KB	Display	PDB format
PDBx/mmJSON format	5dj3.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/dj/5dj3 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/5dj3	HTTPS FTP

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Related structure data

Related structure data	5dj1SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5bk7-4 6c9b-1 6c8t-2 6c9b-2 5bk7-3 5dj1-1 5f9s-d 6c92-1 2hui-d 2huf-d Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: PLP-Dependent L-Arginine Hydroxylase MppP

B: PLP-Dependent L-Arginine Hydroxylase MppP

C: PLP-Dependent L-Arginine Hydroxylase MppP

D: PLP-Dependent L-Arginine Hydroxylase MppP

hetero molecules

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

1

A: PLP-Dependent L-Arginine Hydroxylase MppP

C: PLP-Dependent L-Arginine Hydroxylase MppP

hetero molecules

defined by author&software
83.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: PLP-Dependent L-Arginine Hydroxylase MppP

D: PLP-Dependent L-Arginine Hydroxylase MppP

hetero molecules

defined by author&software
83.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	85.718, 108.277, 195.412
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	PLP-Dependent L-Arginine Hydroxylase MppP Mass: 41537.750 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces wadayamensis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0X1KHF5*PLUS
#2: Chemical	ChemComp-5DK / (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-arginine / PLP-DArg Mass: 403.328 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₂N₅O₇P
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 684 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.73 Å³/Da / Density % sol: 54.93 % / Description: Rectangular plates
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30% PEG 550 MMe, 50mM MgCl2, 100mM HEPES pH 8.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.25→44.53 Å / Num. obs: 79816 / % possible obs: 90.2 % / Redundancy: 3.2 % / R_merge(I) obs: 0.106 / Net I/σ(I): 10
Reflection shell	Resolution: 2.25→2.29 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.726 / Mean I/σ(I) obs: 1.9 / % possible all: 91.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2148: ???)	refinement
HKL-2000	705b	data reduction
HKL-2000	705b	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Holo-MppP (5DJ1)

5dj1

Resolution: 2.227→44.53 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1988	5787	3.78 %	Random
R_work	0.1623	-	-	-
obs	0.1637	-	89.1 %	-

Solvent computation

Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.227→44.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10856	0	109	684	11649

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	11196
X-RAY DIFFRACTION	f_angle_d	1.147	15244
X-RAY DIFFRACTION	f_dihedral_angle_d	12.423	6672
X-RAY DIFFRACTION	f_chiral_restr	0.056	1728
X-RAY DIFFRACTION	f_plane_restr	0.007	2000

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 (%)
2.2269-2.3064	0.2786	495	0.2152	12732	X-RAY DIFFRACTION	77
2.3064-2.3988	0.2517	591	0.1903	15073	X-RAY DIFFRACTION	91
2.3988-2.508	0.2435	587	0.1835	14973	X-RAY DIFFRACTION	90
2.508-2.6402	0.2297	581	0.1762	14808	X-RAY DIFFRACTION	89
2.6402-2.8056	0.2274	580	0.1794	14665	X-RAY DIFFRACTION	89
2.8056-3.0221	0.2239	567	0.1685	14469	X-RAY DIFFRACTION	87
3.0221-3.3262	0.204	562	0.1716	14226	X-RAY DIFFRACTION	86
3.3262-3.8072	0.1887	567	0.1473	14211	X-RAY DIFFRACTION	86
3.8072-4.7958	0.1532	621	0.1309	15812	X-RAY DIFFRACTION	96
4.7958-44.5392	0.1755	636	0.1619	16471	X-RAY DIFFRACTION	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	3.5378	4.3924	-1.9135	5.9145	-3.0812	2.1876	-0.0247	0.191	-0.2225	0.1284	-0.0463	0.0332	-0.0653	0.0838	0.0884	0.2948	0.0407	-0.052	0.2444	-0.1022	0.2134	64.1372	-7.5347	-38.6151
2	0.9996	-0.5043	0.0091	2.5219	1.1874	1.2267	0.0097	-0.0663	-0.2055	0.2041	0.0383	-0.0336	0.3605	0.063	-0.027	0.2804	0.012	-0.0078	0.1963	0.0029	0.2489	66.1469	-5.7745	-18.7501
3	3.7378	3.7138	-5.5081	4.9379	-5.4837	8.3603	-0.0121	0.0908	-0.0434	0.1464	-0.081	-0.0237	-0.3664	-0.135	0.06	0.2359	0.0411	0.0156	0.1731	-0.0415	0.2014	65.1577	15.5365	-16.5093
4	1.9732	0.134	0.6637	1.8337	0.5042	2.8038	-0.0128	0.0168	0.0033	0.0356	0.0449	-0.0665	-0.01	0.1986	-0.0552	0.1948	0.0084	-0.0004	0.2157	-0.0064	0.192	76.3903	8.7297	-14.5056
5	1.2877	0.2048	-0.4467	0.5547	0.791	4.7724	-0.0151	0.1142	-0.1983	-0.0828	0.038	-0.0276	0.0336	0.1042	-0.0346	0.2651	0.003	-0.0172	0.1451	-0.0258	0.2338	64.467	-5.033	-23.285
6	3.4963	0.0016	-0.9775	8.737	2.1001	4.0197	0.0371	0.3921	0.1524	-0.6712	0.0203	-0.3944	-0.1401	0.5254	-0.0109	0.2111	-0.0346	0.0264	0.3866	-0.0161	0.1901	80.0214	12.2878	-38.8524
7	1.8636	0.3049	1.2173	3.8897	2.1904	6.6817	-0.0578	0.4662	0.3439	-0.814	-0.12	0.1655	-0.9235	-0.2048	0.1976	0.3529	-0.0304	-0.0224	0.3153	0.0554	0.2722	69.202	20.7773	-39.6991
8	2.3215	2.875	1.1091	5.0322	1.2978	1.7626	-0.2114	0.559	0.2887	-0.2902	0.1858	-0.0029	-0.1866	0.0077	0.088	0.192	0.0081	0.0477	0.4051	0.1244	0.2277	20.6492	46.8707	-38.8081
9	4.8418	1.6137	-1.8347	1.9937	-1.1958	1.9188	0.0492	-0.0574	0.6743	0.2189	0.1212	0.3424	-0.3731	-0.0283	-0.1888	0.2957	0.0166	0.0142	0.2203	0.0322	0.2977	14.6879	50.8174	-21.2015
10	5.2361	1.528	-0.3868	1.5092	0.3487	0.4382	0.0365	-0.0489	-0.1138	0.125	-0.0239	-0.0148	0.1095	0.0087	-0.0153	0.1995	0.014	0.0061	0.1848	0.038	0.1999	14.7111	26.7794	-13.0373
11	1.1721	-1.1212	1.2931	1.7023	-0.8959	6.155	-0.0245	0.1502	-0.0248	0.0781	0.0428	0.149	-0.2327	-0.2595	0.0254	0.1597	-0.0175	0.0043	0.237	0.0149	0.2257	4.3942	33.8397	-17.9232
12	1.8046	0.4041	-0.2919	0.7547	-0.3674	2.0675	-0.0335	0.1796	0.2824	-0.1132	0.0619	0.0889	-0.1302	-0.1283	-0.0169	0.1959	0.0149	-0.0023	0.1331	0.0302	0.2036	16.0691	44.2258	-20.8105
13	2.6323	-0.2271	0.3561	2.4659	-1.6106	2.7391	0.0963	0.4785	-0.2416	-0.3868	-0.1073	0.3457	0.1915	-0.3812	0.0315	0.263	-0.044	-0.0087	0.4748	-0.0097	0.2641	4.8894	26.897	-39.104
14	2.9745	-0.3126	-1.9808	3.9354	-1.3383	7.6621	0.0976	0.6259	-0.4139	-0.7152	-0.0921	-0.1273	0.9395	0.2484	0.0502	0.3622	0.041	0.0253	0.3735	-0.1111	0.3455	17.5621	15.182	-34.3255
15	3.6077	0.1495	-1.3961	2.2686	-2.3235	6.3069	0.1588	0.9582	-0.1772	-0.9199	-0.0015	0.1632	0.3697	0.0398	-0.1994	0.3805	-0.0021	-0.0104	0.5505	-0.0569	0.2337	12.9355	23.5213	-44.561
16	2.5114	1.529	-3.0068	3.077	-1.8658	4.9491	-0.0567	0.0501	-0.2415	-0.1282	0.1434	0.0351	0.2078	0.224	-0.1471	0.274	0.0163	-0.0344	0.2822	-0.0749	0.3246	51.0362	-13.4256	-35.7147
17	4.2782	-1.0108	-1.4502	0.437	0.6891	1.6645	0.1505	0.3975	0.1977	-0.2047	-0.0245	-0.0258	-0.1171	-0.1931	-0.1564	0.2966	-0.0004	-0.0161	0.2249	-0.0109	0.2405	44.0296	3.9419	-37.4771
18	6.5714	1.1089	-1.0574	2.4252	-0.2508	2.595	-0.0404	-0.1454	0.0489	0.3261	0.0685	0.1407	0.1002	-0.3294	-0.0178	0.2085	-0.0049	0.0146	0.2053	0.0021	0.1283	38.0666	6.5848	-12.7074
19	0.9252	-0.6307	0.4199	5.9997	0.6829	1.4503	0.0177	-0.008	-0.142	0.2312	0.0049	0.3512	0.0523	-0.1806	0.0225	0.183	-0.036	0.019	0.2435	-0.0341	0.2944	30.1584	2.8018	-22.8276
20	2.4058	-2.4307	-1.1249	6.2364	2.5506	2.0865	-0.0214	0.2191	0.0098	-0.0796	0.0675	0.1101	0.0348	-0.0595	-0.0676	0.1875	-0.0274	-0.006	0.2507	0.0117	0.197	40.2105	4.8941	-28.0278
21	3.5872	0.133	0.2784	4.172	1.917	3.4226	0.0347	0.3804	-0.1524	-0.1591	0.1903	-0.2132	0.2367	0.1921	-0.2229	0.1927	-0.0034	-0.0156	0.1885	0.0238	0.1288	49.3117	0.3167	-34.5821
22	3.4915	0.8701	-2.4961	5.4775	-5.0562	5.4738	-0.0327	0.145	-0.4195	-0.0356	0.2885	0.4211	0.7855	-0.329	-0.0584	0.3209	-0.0627	0.0285	0.1937	-0.0778	0.3951	33.1519	-20.6424	-25.7673
23	6.228	1.8075	-1.9024	7.922	-2.822	7.3508	-0.0423	-0.165	-0.5715	0.6595	-0.0714	0.3656	0.0768	-0.4318	0.0597	0.3015	-0.049	0.0919	0.1966	-0.0274	0.3946	29.881	-17.291	-14.5977
24	2.8115	-3.5704	-0.6067	8.4827	1.2799	3.1948	-0.1955	-0.3748	-0.357	0.9375	0.2822	-0.172	0.6852	-0.0241	-0.0396	0.5401	-0.0398	-0.0055	0.3007	0.032	0.3399	40.462	-15.9888	-4.8916
25	5.0233	-0.0426	-4.0289	3.1113	-1.9823	8.504	-0.2578	0.2246	-0.6647	-0.2891	-0.0943	-0.0298	1.0447	-0.1385	0.3621	0.3631	-0.0261	-0.0249	0.2132	-0.0174	0.4146	39.3352	-24.4273	-16.1291
26	2.1805	2.2302	3.1336	3.279	3.4641	5.8254	-0.2224	0.3058	0.2743	-0.3054	0.1518	0.0866	-0.3364	-0.0368	-0.0429	0.2571	-0.0149	-0.0178	0.3245	0.1327	0.3037	33.4746	53.4826	-34.968
27	5.6511	-1.0964	1.7081	1.4258	-1.3704	2.359	0.0649	0.6607	-0.2949	-0.3321	0.0409	0.0314	0.1685	0.3061	-0.1334	0.262	-0.0805	0.0105	0.2961	-0.0359	0.2016	40.9419	36.1943	-34.716
28	1.7	-0.0672	-0.0457	1.0666	-0.3402	1.9919	-0.026	0.0166	-0.0179	0.019	0.0292	-0.131	-0.041	0.19	-0.0116	0.2162	-0.0133	-0.0029	0.2158	-0.0061	0.2273	48.1549	36.1354	-14.6787
29	1.5801	-2.4505	1.8816	4.3538	-4.3032	4.4667	-0.0761	0.1445	0.0293	-0.0079	0.1655	0.0588	-0.2509	-0.0932	0.0382	0.1672	-0.0544	-0.014	0.2641	0.0271	0.2154	39.0551	39.0571	-25.6799
30	3.3512	2.5549	-0.8289	5.0684	-3.6752	4.2076	-0.2715	0.5289	0.133	-0.3235	0.3167	0.0776	-0.0157	-0.1487	-0.0597	0.2106	-0.0048	0.0184	0.2357	-0.0071	0.131	35.2794	39.8364	-32.6267
31	2.1954	0.6585	1.0211	2.7555	1.5485	2.3123	-0.0008	0.1519	0.4615	-0.1369	0.1769	-0.0812	-0.6278	0.1118	-0.228	0.3196	-0.0936	0.0078	0.2485	0.0478	0.3529	51.236	60.6697	-18.1136
32	3.7985	-3.7584	0.9884	8.0966	-2.4159	4.9401	-0.0258	-0.2689	0.4956	0.5371	0.1249	0.281	-0.8587	-0.1089	-0.1062	0.3216	-0.0287	0.0767	0.2315	-0.0269	0.3309	40.9686	58.7138	-3.5024
33	4.2838	-0.55	1.9802	3.5166	2.5429	3.1747	-0.0178	0.0413	0.6477	-0.4313	0.0589	0.3402	-0.6917	-0.189	0.0192	0.3744	-0.0325	0.0435	0.2225	0.0634	0.4372	43.0037	66.2845	-15.2275

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 23 through 54 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 55 through 103 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 104 through 124 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 125 through 218 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 219 through 272 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 273 through 313 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 314 through 373 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 23 through 54 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 55 through 89 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 90 through 156 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 157 through 201 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 202 through 272 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 273 through 313 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 314 through 349 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 350 through 373 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 23 through 54 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 55 through 89 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 90 through 156 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 157 through 201 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 202 through 242 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 243 through 272 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 273 through 292 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 293 through 313 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 314 through 349 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 350 through 373 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 23 through 54 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 55 through 89 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 90 through 218 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 219 through 242 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 243 through 272 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 273 through 313 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 314 through 349 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 350 through 373 )

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