PDB-6c9b: The structure of MppP soaked with the products 4HKA and 2KA

ID or keywords:

Entry

Database: PDB / ID: 6c9b

Title

The structure of MppP soaked with the products 4HKA and 2KA

Components

PLP-Dependent L-Arginine Hydroxylase MppP

Keywords

oxidoreductase/oxidoreductase inhibitor / dimer / product 4HKA binding complex / oxidase / PLP / ANTIBIOTIC / oxidoreductase-oxidoreductase inhibitor complex

Function / homology

Function and homology information

biosynthetic process / pyridoxal phosphate binding / metal ion binding
Similarity search - Function

Biological species

Streptomyces wadayamensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.689 Å

Authors

Han, L. / Silvaggi, N.R.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2018
Title: Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase.
Authors: Han, L. / Vuksanovic, N. / Oehm, S.A. / Fenske, T.G. / Schwabacher, A.W. / Silvaggi, N.R.

History

Deposition	Jan 26, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 4, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 20, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 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 1.4	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	6c9b.cif.gz	814 KB	Display	PDBx/mmCIF format
PDB format	pdb6c9b.ent.gz	686.9 KB	Display	PDB format
PDBx/mmJSON format	6c9b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6c9b_validation.pdf.gz	466.7 KB	Display	wwPDB validaton report
Full document	6c9b_full_validation.pdf.gz	474.6 KB	Display
Data in XML	6c9b_validation.xml.gz	59.8 KB	Display
Data in CIF	6c9b_validation.cif.gz	87 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c9/6c9b ftp://data.pdbj.org/pub/pdb/validation_reports/c9/6c9b	HTTPS FTP

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Related structure data

Related structure data	5bk7C 6c8tC 6c92C 5dj1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5dj3-1 5bk7-3 6c8t-2 5bk7-4 5dj1-2 2hoz-d 6c92-1 2hp2-d 6xvp-d 3v4x-5 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
Evidence: gel filtration
83.8 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)

Unit cell

Length a, b, c (Å)	86.110, 108.830, 195.170
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) / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0X1KHF5
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-EGV / (4S)-5-carbamimidamido-4-hydroxy-2-oxopentanoic acid Mass: 189.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₁N₃O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 997 / 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: 2.74 Å³/Da / Density % sol: 55.06 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30% polyethylene glycol monomethyl ether 550 (PEG MME 550), 50 mM MgCl2, and 0.1 M 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: 0.978 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 15, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 1.689→50 Å / Num. obs: 199364 / % possible obs: 97.3 % / Redundancy: 6.5 % / R_merge(I) obs: 0.063 / Net I/σ(I): 21.8
Reflection shell	Resolution: 1.69→1.72 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.488 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 9240 / % possible all: 92.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
Aimless		data scaling
iMOSFLM		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5DJ1

5dj1

Resolution: 1.689→48.792 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.37 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1652	1998	1 %
R_work	0.1507	-	-
obs	0.1509	199127	97.04 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.689→48.792 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11117	0	16	997	12130

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11406
X-RAY DIFFRACTION	f_angle_d	1.041	15539
X-RAY DIFFRACTION	f_dihedral_angle_d	18.917	6788
X-RAY DIFFRACTION	f_chiral_restr	0.059	1764
X-RAY DIFFRACTION	f_plane_restr	0.007	2037

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 (%)
1.689-1.7313	0.2479	133	0.2241	13196	X-RAY DIFFRACTION	92
1.7313-1.7781	0.2626	135	0.206	13341	X-RAY DIFFRACTION	93
1.7781-1.8304	0.2106	137	0.1933	13576	X-RAY DIFFRACTION	94
1.8304-1.8895	0.1761	140	0.1728	13727	X-RAY DIFFRACTION	96
1.8895-1.957	0.2063	141	0.1679	13943	X-RAY DIFFRACTION	96
1.957-2.0354	0.1763	141	0.1568	13937	X-RAY DIFFRACTION	97
2.0354-2.128	0.1603	144	0.143	14088	X-RAY DIFFRACTION	98
2.128-2.2402	0.1614	143	0.1418	14169	X-RAY DIFFRACTION	98
2.2402-2.3805	0.1672	142	0.1391	14043	X-RAY DIFFRACTION	97
2.3805-2.5643	0.1593	146	0.1403	14403	X-RAY DIFFRACTION	99
2.5643-2.8224	0.1468	147	0.1445	14485	X-RAY DIFFRACTION	100
2.8224-3.2307	0.1841	148	0.1442	14595	X-RAY DIFFRACTION	100
3.2307-4.07	0.1434	150	0.136	14702	X-RAY DIFFRACTION	100
4.07-48.8128	0.1542	151	0.1569	14924	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	0.3254	-0.0571	-0.9756	0.8113	0.252	3.0744	-0.1136	0.0033	-0.1988	0.1763	0.1571	0.0982	0.0499	0.4028	-0.0365	0.365	-0.0144	0.042	0.223	-0.0778	0.3805	-39.3568	-17.7199	-23.2997
2	0.8315	-0.2611	-0.1589	0.7304	0.1757	0.6142	0.0053	0.0899	-0.0635	-0.0096	-0.0324	0.1515	0.0801	-0.0838	0.0089	0.182	-0.0265	0.0159	0.1763	-0.0542	0.2233	-45.4851	2.8427	-26.4935
3	0.7706	0.023	-0.2673	0.6144	-0.1726	1.8815	-0.0343	-0.021	-0.3566	0.1719	0.0166	0.4427	0.2515	-0.2675	-0.1267	0.4018	-0.1411	0.1159	0.1966	-0.0798	0.5183	-54.4738	-19.197	-20.3604
4	0.2844	-0.0724	0.0473	1.3964	-0.1458	0.3245	-0.0799	-0.1502	-0.2727	0.5653	0.0403	0.0134	0.3654	0.0187	0.0183	0.5698	-0.0304	0.0976	0.1975	0.0218	0.417	-46.0223	-19.7366	-9.2435
5	0.544	0.452	0.2037	0.4118	-0.0031	1.2091	-0.0522	0.1891	0.0486	0.0601	-0.019	0.3452	-0.0619	-0.2734	-0.0046	0.2648	-0.0128	0.0183	0.3984	-0.0505	0.2689	-24.0639	11.6271	-37.8136
6	2.7408	1.9387	-1.5885	1.6613	-1.1401	1.9133	0.0103	0.1302	-0.4282	-0.0595	-0.0326	-0.1987	0.2661	0.1603	0.0469	0.3141	0.053	-0.011	0.2128	-0.1237	0.3095	-23.5298	-15.9495	-37.2259
7	1.049	0.3158	0.2824	0.6803	0.1396	0.7175	0.079	-0.0615	-0.0167	0.1805	-0.0736	0.0215	0.0954	0.0828	-0.0012	0.2023	-0.0103	0.0098	0.1741	-0.0172	0.1623	-17.6572	5.1913	-16.1687
8	0.8253	0.0498	0.2768	0.4781	-0.1504	3.0559	0.0573	0.0654	-0.0296	0.1879	-0.0478	-0.1001	0.0192	0.3581	-0.0243	0.1956	-0.0087	-0.0323	0.2273	-0.0134	0.194	-5.5247	9.2816	-14.465
9	0.9609	0.1847	0.3689	0.6183	0.0989	0.6563	0.0658	0.0686	-0.1799	0.1128	-0.0296	-0.0389	0.1631	0.1498	-0.0258	0.2479	0.0162	-0.006	0.1956	-0.034	0.205	-16.9483	-2.0136	-20.5469
10	1.2946	-0.1396	0.0628	3.2864	0.9767	1.099	-0.0472	0.3672	0.0508	-0.3123	0.1545	-0.3778	-0.099	0.3891	-0.029	0.2096	-0.0336	0.05	0.3975	-0.0126	0.2141	-5.706	12.1491	-38.7808
11	0.7142	0.1952	0.5662	1.0373	0.7349	2.6063	-0.047	0.268	0.3286	-0.3995	-0.11	0.1757	-0.6658	-0.1758	0.1247	0.3497	0.0233	-0.0287	0.2926	0.0733	0.2847	-18.6624	24.2862	-36.1574
12	1.3941	0.0771	-0.0112	2.0625	0.1959	2.0619	-0.1201	0.6281	0.1482	-0.527	0.1408	-0.0242	-0.2653	0.2534	0.0125	0.3311	-0.0794	0.0015	0.469	0.0333	0.2054	-13.1451	16.0853	-45.4231
13	0.6338	0.2379	0.7257	0.313	0.2659	0.8183	-0.1359	0.2534	0.2674	-0.1217	0.1221	0.1014	-0.2106	-0.0744	0.0548	0.3401	-0.1246	-0.0406	0.3618	0.1935	0.2504	-52.7004	54.0477	-34.6709
14	1.3036	-0.1711	0.1975	0.4046	-0.3361	0.4614	-0.0423	0.4216	-0.1483	-0.1778	0.0632	-0.031	0.0216	0.1611	-0.0222	0.2297	-0.0929	0.0144	0.3377	-0.0099	0.1925	-45.0103	36.5783	-34.7288
15	0.7206	0.199	0.2184	0.7633	-0.0901	0.9135	-0.0257	0.106	0.0351	-0.0044	0.0518	-0.111	-0.051	0.1822	-0.0319	0.1469	-0.0375	-0.0173	0.1879	0.0127	0.1887	-37.8843	37.027	-13.3268
16	0.6623	0.1796	0.191	0.6648	-0.2436	0.6812	-0.1369	0.3281	0.0705	-0.1071	0.143	-0.0471	-0.1267	0.1225	-0.0092	0.1753	-0.067	-0.0043	0.2439	0.0381	0.155	-45.854	38.1459	-27.752
17	0.4565	-0.4208	0.1084	0.6532	0.7135	2.5623	-0.0937	0.2217	0.3042	-0.1521	0.1098	-0.1575	-0.424	0.0857	0.0015	0.3786	-0.2159	-0.0255	0.2583	0.1474	0.3373	-35.7766	62.1846	-23.863
18	1.7745	0.4162	0.6365	2.2597	0.6524	1.7895	0.0181	0.0605	0.1233	0.1438	0.1331	-0.3218	-0.2407	0.2876	-0.1289	0.3718	-0.1497	-0.0386	0.2431	0.031	0.3344	-33.2646	59.9965	-12.2896
19	0.7448	-1.0012	0.1678	3.1145	-0.8452	1.1354	-0.0803	-0.1738	0.2245	0.5305	0.2727	0.3798	-0.6896	-0.0325	-0.1605	0.4818	-0.0092	0.0405	0.2077	0.0111	0.3296	-44.7621	59.1338	-3.5997
20	0.9623	0.0873	0.2103	1.3988	0.6526	2.0246	-0.0939	0.1045	0.3858	-0.0291	0.1881	0.2412	-0.6265	-0.0522	-0.0413	0.4769	-0.0611	0.0057	0.2013	0.0905	0.4207	-42.5919	67.3244	-14.335
21	1.0688	0.634	-0.2621	0.528	-0.4635	0.6723	-0.1125	0.4317	0.3052	-0.0804	0.0969	0.0599	-0.2291	-0.0198	-0.0114	0.2587	-0.0281	-0.0123	0.3152	0.1525	0.2726	-67.6904	49.7972	-32.8848
22	1.337	0.2563	-0.0504	0.3077	-0.1925	0.6557	0.0051	0.0493	0.0523	0.0771	-0.0209	-0.0118	-0.0864	-0.0198	0.0014	0.1587	-0.0151	-0.0007	0.1503	0.0144	0.1546	-67.8035	34.9995	-15.2553
23	1.0255	0.1352	-0.0434	0.7233	-0.2763	1.0379	-0.0165	0.1372	0.0328	0.055	0.0104	0.1147	-0.0762	-0.17	0.0079	0.1547	0.0046	0.0206	0.1989	0.0171	0.1759	-80.3334	32.5491	-14.8212
24	0.7587	0.0739	-0.1522	0.5863	-0.4007	1.0988	-0.0419	0.22	0.2926	-0.0158	0.0643	0.0596	-0.205	-0.1566	-0.0003	0.2297	-0.0076	-0.0009	0.1973	0.0753	0.2113	-67.178	45.3304	-23.2662
25	0.9589	-0.19	0.0507	2.3735	-0.736	0.9218	-0.0316	0.6311	-0.1207	-0.3681	0.0944	0.3191	0.1188	-0.1993	0.0189	0.2103	-0.067	-0.0401	0.5131	-0.0316	0.1981	-81.2832	27.2556	-38.9645
26	0.5523	-0.0854	-0.1141	1.3057	-0.0936	1.523	0.0858	0.6693	-0.3554	-0.3529	-0.0374	-0.0951	0.3689	0.2449	-0.0067	0.2745	0.0004	0.04	0.5384	-0.1522	0.2733	-70.3601	18.4074	-38.3638

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 23:35 )	A	23 - 35
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 36:272 )	A	36 - 272
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 273:313 )	A	273 - 313
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 314:375 )	A	314 - 375
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 7:35 )	B	7 - 35
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 36:54 )	B	36 - 54
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 55:156 )	B	55 - 156
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 157:181 )	B	157 - 181
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 182:272 )	B	182 - 272
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 273:313 )	B	273 - 313
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 314:349 )	B	314 - 349
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 350:375 )	B	350 - 375
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 23:54 )	C	23 - 54
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 55:89 )	C	55 - 89
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 90:201 )	C	90 - 201
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 202:272 )	C	202 - 272
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 273:292 )	C	273 - 292
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 293:313 )	C	293 - 313
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 314:349 )	C	314 - 349
20	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 350:375 )	C	350 - 375
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 23:72 )	D	23 - 72
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 73:127 )	D	73 - 127
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 128:218 )	D	128 - 218
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 219:272 )	D	219 - 272
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 273:313 )	D	273 - 313
26	X-RAY DIFFRACTION	26	( CHAIN D AND RESID 314:375 )	D	314 - 375

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi