PDB-5dj1: Structure of the PLP-Dependent L-Arginine Hydroxylase MppP Holoenzyme

ID or keywords:

Entry

Database: PDB / ID: 5dj1

Title

Structure of the PLP-Dependent L-Arginine Hydroxylase MppP Holoenzyme

Components

PLP-Dependent L-Arginine Hydroxylase MppP

Keywords

TRANSFERASE / aminotransferase / enduracididine / hydroxylase / pyridoxal 5'-phosphate

Function / homology

Function and homology information

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

Biological species

Streptomyces wadayamensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.102 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	May 3, 2017	Group: Non-polymer description
Revision 1.3	Apr 2, 2025	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5dj1.cif.gz	801.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5dj1.ent.gz	681.6 KB	Display	PDB format
PDBx/mmJSON format	5dj1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5dj1_validation.pdf.gz	447.6 KB	Display	wwPDB validaton report
Full document	5dj1_full_validation.pdf.gz	454.7 KB	Display
Data in XML	5dj1_validation.xml.gz	70.5 KB	Display
Data in CIF	5dj1_validation.cif.gz	94.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dj/5dj1 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/5dj1	HTTPS FTP

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Related structure data

Related structure data	5dj3C C: citing same article (ref.)
Similar structure data	5dj3-2 6c8t-2 2huf-d 6c92-2 5dj3-1 4cbs-1 2hui-d 6c92-1 5luc-2 6c3b-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

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

1

A: PLP-Dependent L-Arginine Hydroxylase MppP

B: PLP-Dependent L-Arginine Hydroxylase MppP

hetero molecules

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

2

C: PLP-Dependent L-Arginine Hydroxylase MppP

D: PLP-Dependent L-Arginine Hydroxylase MppP

hetero molecules

defined by author&software
83.6 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: 41765.867 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-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#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 Mass: 18.015 Da / Num. of mol.: 923 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.68 % / 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-D / Wavelength: 0.98178 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98178 Å / Relative weight: 1
Reflection	Resolution: 2.1→41.45 Å / Num. obs: 106188 / % possible obs: 100 % / Redundancy: 14.4 % / R_merge(I) obs: 0.106 / Net I/σ(I): 30.7
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 11.5 % / R_merge(I) obs: 0.734 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Streptomyces globisporus MppP

Resolution: 2.102→41.45 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1711	5256	4.96 %	Random
R_work	0.1436	-	-	-
obs	0.1449	106072	99.74 %	-

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.102→41.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11060	0	5	923	11988

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	11335
X-RAY DIFFRACTION	f_angle_d	1.059	15447
X-RAY DIFFRACTION	f_dihedral_angle_d	11.772	6755
X-RAY DIFFRACTION	f_chiral_restr	0.057	1750
X-RAY DIFFRACTION	f_plane_restr	0.007	2031

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 (%)
2.1022-2.1773	0.2024	482	0.1566	9768	X-RAY DIFFRACTION	98
2.1773-2.2645	0.1807	546	0.141	9973	X-RAY DIFFRACTION	100
2.2645-2.3676	0.1763	510	0.138	10030	X-RAY DIFFRACTION	100
2.3676-2.4924	0.1772	519	0.1365	10020	X-RAY DIFFRACTION	100
2.4924-2.6485	0.1896	545	0.1396	10008	X-RAY DIFFRACTION	100
2.6485-2.853	0.1876	549	0.1464	10038	X-RAY DIFFRACTION	100
2.853-3.14	0.171	524	0.149	10104	X-RAY DIFFRACTION	100
3.14-3.5941	0.1749	531	0.1463	10101	X-RAY DIFFRACTION	100
3.5941-4.5273	0.1464	518	0.1277	10243	X-RAY DIFFRACTION	100
4.5273-41.4582	0.1647	532	0.1563	10531	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	1.8371	-2.0232	-0.0002	3.0243	0.0926	1.7106	-0.2175	-0.4146	0.0731	0.0723	0.1605	0.0454	-0.1075	0.0182	0.0325	0.2314	0.0459	0.0027	0.3491	-0.136	0.2133	65.0227	46.3679	38.5812
2	0.4695	0.225	-0.1178	0.5339	0.3423	0.5018	-0.0142	-0.0637	0.3145	-0.1243	0.0659	-0.039	-0.4482	0.0542	0.0309	0.2392	-0.0158	-0.0065	0.1216	-0.0612	0.2173	68.9576	46.7495	19.2051
3	5.8004	-1.3307	2.7027	3.6915	-2.1523	2.4577	0.0157	-0.2048	-0.2504	-0.0784	-0.0117	0.0964	0.1873	-0.0362	0.023	0.1061	0.0135	0.0117	0.0855	-0.0274	0.1302	67.7782	25.246	15.3946
4	1.2374	-0.3539	-0.1714	1.2173	0.3773	1.6961	-0.0412	-0.1256	0.1453	-0.02	0.042	-0.1243	-0.1734	0.2051	-0.0342	0.1189	-0.014	-0.0013	0.1168	-0.0302	0.1356	74.8467	37.0926	18.1411
5	1.6796	0.624	-0.0883	4.7572	0.8595	0.9539	0.0334	-0.4916	-0.161	0.652	0.0294	-0.4732	0.234	0.3252	0.0619	0.2733	0.0822	-0.0637	0.4557	0.0136	0.2053	81.2599	27.0035	39.0034
6	1.7818	0.4209	-0.2367	3.3128	0.4538	3.2119	0.0915	-0.6797	-0.421	0.7412	-0.0205	0.1494	0.5309	-0.2434	-0.0572	0.3219	0.0346	0.0418	0.3961	0.1293	0.299	70.3333	18.2015	37.9816
7	0.5847	-0.3064	0.9108	1.2939	-0.5155	1.4981	-0.0813	-0.0753	0.2546	0.0027	0.1103	0.0413	-0.2624	0.0273	0.2786	0.3247	0.1446	-0.0531	0.395	-0.2329	0.2098	52.0108	53.3921	34.9215
8	4.0533	0.3636	0.1785	1.1401	0.4944	0.4934	-0.0259	-0.5286	-0.2829	0.1882	-0.0174	-0.0077	0.05	-0.4633	0.0658	0.2122	0.0876	-0.0003	0.3506	-0.0285	0.1609	44.6833	35.9131	34.6461
9	0.7546	-0.2133	-0.0703	0.7255	0.0983	1.1166	-0.061	-0.204	0.0488	0.0214	0.0125	0.1481	-0.1262	-0.3978	0.0279	0.1329	0.0564	-0.0229	0.2491	-0.0488	0.1682	40.8716	36.9918	19.0064
10	0.2402	0.121	-0.2376	0.1025	0.0581	1.1011	-0.0822	-0.1023	0.2823	-0.0828	0.0776	0.0242	-0.3462	-0.0694	-0.1863	0.3376	0.3964	-0.0364	0.3575	-0.4003	0.3611	35.1994	61.6262	23.8266
11	3.4172	-0.6412	0.4742	4.3025	-0.8075	3.3514	-0.0903	-0.1021	0.2093	0.0381	0.249	0.3655	-0.4055	-0.4216	-0.2264	0.2863	0.1736	-0.0707	0.3099	-0.0752	0.3476	32.925	59.47	12.2181
12	3.1127	2.4482	1.1748	2.388	2.2284	4.1292	-0.147	0.2847	0.4048	-0.6316	0.3447	-0.3766	-1.0057	0.173	-0.2266	0.4287	0.0404	0.0258	0.2592	-0.0356	0.3568	44.5887	58.7047	3.5849
13	0.943	0.0608	-0.9891	1.9402	-0.757	1.3059	-0.0968	-0.2826	0.503	0.2365	0.2411	-0.1493	-0.9463	0.215	-0.1438	0.487	0.0994	-0.0452	0.2525	-0.1337	0.4029	42.3298	66.5415	14.8494
14	2.1828	1.2545	-2.048	2.4436	-1.5553	2.4053	-0.0522	0.0717	-0.2361	-0.0751	0.0671	0.0356	0.1763	0.0954	-0.0145	0.3003	0.0324	0.0023	0.2238	-0.114	0.2731	50.8517	40.512	62.0112
15	1.8372	-0.1778	-0.4862	0.9889	0.1907	1.9157	0.0103	0.1386	0.0591	-0.0709	0.0115	0.0594	-0.1026	-0.1525	-0.0056	0.1495	0.005	0.0072	0.0918	-0.0193	0.1581	43.1239	59.1996	69.4983
16	4.9804	0.3165	0.558	1.5978	-0.2789	2.5353	-0.0652	-0.3633	-0.0954	0.2783	0.1023	0.3273	0.068	-0.3636	-0.0036	0.1989	-0.0094	0.0877	0.1754	-0.0161	0.1865	34.1046	60.0227	86.1965
17	1.3969	0.0744	0.2417	3.9584	0.5629	1.5084	-0.0475	0.0646	-0.1059	0.132	-0.0112	0.4635	0.1015	-0.2514	0.0375	0.1549	-0.0259	0.0371	0.1816	-0.0305	0.2805	29.5504	56.669	74.761
18	2.0982	-0.0873	-0.147	1.8815	0.5726	1.7742	-0.0176	0.1181	-0.0403	-0.1022	0.0519	0.1413	0.0218	-0.1041	-0.0324	0.1314	-0.0063	0.0372	0.138	-0.0066	0.1597	40.0283	58.3483	69.9839
19	3.2243	1.055	0.35	3.5594	1.2969	2.9777	-0.0808	0.402	-0.1337	-0.3712	0.2442	0.0006	-0.0392	0.062	-0.1031	0.1499	0.0213	-0.0069	0.124	-0.0056	0.1085	48.9437	54.2521	63.1191
20	1.026	-0.9623	0.065	1.6081	-1.391	5.3934	-0.155	0.1572	-0.527	-0.1184	0.2323	0.3211	0.8891	-0.3575	-0.0948	0.3785	-0.0875	0.0081	0.2191	-0.083	0.4855	32.8812	33.0847	71.8011
21	3.419	0.8069	-0.0575	4.8823	-1.9242	2.1755	0.0047	-0.1649	-0.3426	0.263	0.1645	0.5773	0.5291	-0.5665	-0.3426	0.4059	-0.1367	0.0903	0.2383	-0.02	0.4863	29.3083	36.15	82.8751
22	1.838	-0.9811	-0.1909	5.7828	-0.8304	1.7948	-0.0601	-0.5006	-0.4924	1.0768	0.1026	0.1356	0.7223	0.1331	-0.0714	0.6587	-0.0162	-0.0104	0.3	0.0624	0.373	40.1305	37.8313	92.6857
23	1.3664	0.2339	0.8902	2.1583	-0.5458	0.8237	-0.0712	-0.0668	-0.7264	0.0281	0.0637	-0.0039	0.8149	0.0749	-0.1322	0.5059	0.005	0.0441	0.1375	0.0183	0.4801	38.897	28.8288	82.395
24	2.0721	2.4038	-0.8926	3.1498	-0.7007	2.1062	-0.1355	0.1597	-0.21	-0.1304	0.0701	0.0501	0.1689	0.1826	0.082	0.2307	0.0375	-0.0297	0.2368	-0.1102	0.2056	63.9311	47.0375	59.1539
25	1.3056	0.6932	0.0611	1.3849	0.503	0.786	0.1067	-0.1875	-0.4144	0.3607	-0.049	-0.0718	0.4233	0.1996	-0.0104	0.2871	0.0299	-0.0261	0.1409	0.0106	0.2144	65.935	48.2021	78.9244
26	6.177	0.795	-2.0789	1.8091	-0.5846	2.4381	0.0196	0.0664	0.3627	0.2462	-0.0215	0.0882	-0.2687	-0.0399	0.0395	0.2279	-0.061	0.0375	0.1463	-0.0368	0.1579	64.6855	69.5575	81.2336
27	1.9035	0.5872	0.2574	1.5095	0.29	1.6169	0.0952	-0.0818	-0.1078	0.2275	-0.0773	-0.1277	0.0553	0.2686	-0.0119	0.2102	-0.0018	-0.0244	0.1618	0.0036	0.1406	71.6945	57.8944	79.8998
28	2.4708	-0.5514	-0.4604	7.8786	0.2382	1.5682	-0.0245	0.4071	0.1529	-0.5992	0.0141	-0.5983	-0.1745	0.5804	0.1236	0.2348	-0.0876	0.0259	0.4486	0.0108	0.1962	79.5642	66.7245	58.9064
29	1.4961	-0.1548	-0.515	2.0131	0.284	3.4611	-0.0084	0.5592	0.3749	-0.7876	-0.0159	0.3872	-0.8439	-0.0669	0.0003	0.4555	-0.0712	-0.086	0.3582	0.0677	0.2886	68.2918	75.0068	58.3227

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 272 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 273 through 313 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 314 through 373 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 23 through 54 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 55 through 89 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 90 through 272 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 273 through 292 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 293 through 313 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 314 through 349 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 350 through 374 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 23 through 54 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 55 through 115 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 116 through 156 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 157 through 201 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 202 through 242 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 243 through 272 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 273 through 292 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 293 through 313 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 314 through 349 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 350 through 375 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 23 through 54 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 55 through 103 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 104 through 124 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 125 through 272 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 273 through 313 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 314 through 373 )

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About Yorodumi

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Yorodumi