PDB-6c92: The structure of MppP soaked with the product 2-ketoarginine

ID or keywords:

Entry

Database: PDB / ID: 6c92

Title

The structure of MppP soaked with the product 2-ketoarginine

Components

(PLP-Dependent L-Arginine Hydroxylase MppP) x 2

Keywords

OXIDOREDUCTASE / dimer / product 2KA binding complex / oxidase / PLP

Function / homology

Function and homology information

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

Biological species

Streptomyces wadayamensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.834 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 25, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 5, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	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 1.3	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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PDBx/mmCIF format	6c92.cif.gz	823.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6c92.ent.gz	693 KB	Display	PDB format
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Validation report

Summary document	6c92_validation.pdf.gz	908.3 KB	Display	wwPDB validaton report
Full document	6c92_full_validation.pdf.gz	929 KB	Display
Data in XML	6c92_validation.xml.gz	64 KB	Display
Data in CIF	6c92_validation.cif.gz	91.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c9/6c92 ftp://data.pdbj.org/pub/pdb/validation_reports/c9/6c92	HTTPS FTP

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Related structure data

Related structure data	5bk7C 6c8tC 6c9bC 5dj1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6c8t-2 5dj1-2 5bk7-1 5bk7-4 5dj3-1 5bk7-3 5hhy-d 6c9b-1 5dj1-1 2ch2-2 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

B: PLP-Dependent L-Arginine Hydroxylase MppP

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.859, 108.780, 195.519
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.: 1 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
#2: Protein	PLP-Dependent L-Arginine Hydroxylase MppP Mass: 41765.867 Da / Num. of mol.: 3 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
#3: Chemical	ChemComp-EQJ / (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine Mass: 403.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₂N₅O₇P
#4: Chemical	ChemComp-EGV / (4S)-5-carbamimidamido-4-hydroxy-2-oxopentanoic acid Mass: 189.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₁N₃O₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1032 / 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: 55.05 %
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: 1.83→44.59 Å / Num. obs: 160466 / % possible obs: 99.9 % / Redundancy: 6.6 % / R_merge(I) obs: 0.074 / Net I/σ(I): 14.4
Reflection shell	Resolution: 1.83→1.87 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.567 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 7902 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5DJ1

5dj1

Resolution: 1.834→44.585 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.14

	R_factor	Num. reflection	% reflection
R_free	0.1754	2000	1.25 %
R_work	0.1515	-	-
obs	0.1518	160324	99.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.834→44.585 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11237	0	51	1032	12320

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	11581
X-RAY DIFFRACTION	f_angle_d	1.143	15779
X-RAY DIFFRACTION	f_dihedral_angle_d	18.949	6895
X-RAY DIFFRACTION	f_chiral_restr	0.073	1786
X-RAY DIFFRACTION	f_plane_restr	0.007	2074

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 (%)
1.834-1.8799	0.2575	141	0.2197	11217	X-RAY DIFFRACTION	100
1.8799-1.9307	0.2051	142	0.1951	11197	X-RAY DIFFRACTION	100
1.9307-1.9875	0.1953	141	0.1722	11175	X-RAY DIFFRACTION	100
1.9875-2.0517	0.2164	142	0.1643	11243	X-RAY DIFFRACTION	100
2.0517-2.125	0.1888	141	0.1561	11201	X-RAY DIFFRACTION	100
2.125-2.2101	0.2092	143	0.1543	11233	X-RAY DIFFRACTION	100
2.2101-2.3106	0.1582	142	0.15	11279	X-RAY DIFFRACTION	100
2.3106-2.4325	0.1867	142	0.1445	11219	X-RAY DIFFRACTION	100
2.4325-2.5848	0.1642	142	0.1454	11244	X-RAY DIFFRACTION	100
2.5848-2.7844	0.1778	143	0.1476	11341	X-RAY DIFFRACTION	100
2.7844-3.0645	0.1793	143	0.1451	11330	X-RAY DIFFRACTION	100
3.0645-3.5078	0.1626	143	0.1439	11383	X-RAY DIFFRACTION	100
3.5078-4.4189	0.1509	146	0.1323	11462	X-RAY DIFFRACTION	100
4.4189-44.5986	0.1703	149	0.1614	11800	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	0.0034	0.0052	-0.0033	0.0084	-0.0067	0.0039	-0.0594	-0.0001	-0.0868	0.0917	0.0231	0.0229	-0.033	0.0144	0	0.3734	-0.0167	0.0527	0.1708	-0.038	0.3637	-36.8993	-15.4102	-17.2811
2	0.0045	-0.0027	-0.0082	0.0027	0.0045	0.0068	0.0303	0.0652	-0.0394	-0.0023	-0.0309	0.0336	0.0346	0.0436	0.0061	0.2624	0.0184	0.0115	0.2449	-0.1131	0.2031	-31.6562	-10.9009	-43.1875
3	0.0025	-0.0037	0.0006	0.007	0.0053	0.0059	-0.0039	0.1066	0.0192	-0.1206	-0.0268	0.0722	0.0153	-0.0349	-0	0.2063	-0.0091	0.0063	0.2048	-0.0576	0.209	-43.227	3.8579	-39.2379
4	0.0297	-0.0168	0.0193	0.0293	-0.0166	0.0153	-0.0228	-0.0036	-0.0333	0.0716	-0.0182	0.0526	0.049	-0.0401	-0.0031	0.1554	-0.0162	0.0534	0.1335	-0.0373	0.1835	-46.973	6.4113	-14.3113
5	0.0259	-0.0005	-0.0197	0.0152	0.0037	0.0224	-0.0016	0.123	-0.0497	-0.0113	-0.0369	0.1766	0.0197	-0.1167	-0.0001	0.1725	-0.0336	0.0288	0.1813	-0.0642	0.2883	-54.7584	4.5897	-24.3574
6	0.0122	-0.0037	-0.0046	0.0022	-0.0008	0.004	-0.0456	0.0717	-0.0272	-0.0128	0.0436	0.0255	0.0111	-0.0586	-0	0.1706	-0.001	0.0219	0.144	-0.0505	0.2159	-41.1278	1.697	-28.4094
7	0.0085	-0.0096	-0.0078	0.0098	0.0055	0.0104	0.0091	0.1196	0.0134	-0.0353	-0.009	0.0302	0.0346	-0.0163	0.0047	0.1721	-0.0123	0.0053	0.1477	-0.0687	0.1667	-36.541	0.2371	-34.6935
8	0.0089	0.0002	-0.0022	0.0028	0.0017	0.0009	-0.0422	0.0376	-0.054	0.0355	-0.0121	0.0626	0.0302	-0.02	-0.0147	0.3626	-0.1445	0.0972	0.1101	-0.1471	0.4766	-52.6006	-20.7361	-25.7691
9	0.0032	-0.0003	-0.0008	0	0.0001	-0	0.0039	-0.0312	-0.0441	0.0469	0.0132	0.0495	0.0072	-0.0291	0.0019	0.3397	-0.1003	0.1416	0.1781	-0.0148	0.4336	-55.9772	-17.6496	-14.5664
10	0.0152	0.0034	0.0097	0.0192	-0.0204	0.0314	0.0069	-0.0569	-0.0302	0.0674	-0.014	-0.007	0.0776	-0.0165	-0.0003	0.4441	-0.0332	0.1138	0.1319	0.0623	0.2828	-45.1149	-16.0029	-5.0088
11	-0.0007	0.0007	-0.0015	0.0118	-0.0036	0.0032	0.0033	-0.0008	-0.0493	0.0075	0.0256	-0.0031	0.0295	-0.0066	0.0135	0.4699	-0.0521	0.1249	0.0656	-0.015	0.431	-46.5062	-25.0629	-15.2121
12	0.0065	0.0049	-0.0016	0.0055	-0.007	0.011	-0.0427	0.045	0.0035	0.0179	0.0359	0.0493	0.0014	-0.0316	0	0.2269	-0.0154	0.0154	0.3248	-0.0637	0.2036	-23.9783	11.4913	-37.7768
13	0.0054	0.0045	0.0035	0.0058	0.002	0.0013	0.011	0.0763	-0.1621	0.0246	-0.0139	-0.0494	0.1416	0.0663	-0.0128	0.2855	0.0468	-0.001	0.194	-0.0801	0.285	-20.3801	-14.5675	-29.9725
14	0.0071	0.0094	0.0014	0.0104	-0.002	0.0109	0.1212	-0.0938	-0.0243	0.0996	-0.0639	0.0315	0.1073	0.0556	0.0001	0.2087	0.0032	-0.0041	0.1542	-0.0204	0.1727	-21.1644	-1.2029	-15.8509
15	0.0241	-0.0069	0.0088	0.0104	-0.0098	0.0136	-0.0143	-0.0043	0.0823	0.1162	-0.0353	0.0387	-0.0147	0.0638	-0.0008	0.2047	-0.0375	0.0199	0.2039	-0.0405	0.189	-15.6022	16.2208	-13.6917
16	0.0023	0.0044	0.0012	0.0206	0.0038	0.0021	0.0487	0.0492	-0.0381	0.0907	-0.0176	-0.0492	-0.0094	0.0539	0	0.1921	-0.0165	-0.0181	0.2503	-0.007	0.1814	-5.4648	9.3246	-14.3703
17	0.046	0.0249	0.0354	0.0699	-0.0257	0.0443	0.0551	0.0341	-0.1436	0.1009	-0.0312	-0.0136	0.1176	0.1354	-0.0014	0.2285	0.0155	-0.0063	0.1949	-0.037	0.1915	-16.91	-2.0579	-20.518
18	0.0032	-0.0019	-0.0093	0.006	0.0087	0.0145	-0.007	0.1634	-0.0296	-0.0734	0.0302	-0.0783	-0.0209	0.1642	0	0.1825	-0.0242	0.033	0.346	-0.0202	0.1738	-5.6905	12.072	-38.7353
19	0.0273	-0.0024	0.0129	0.0086	-0.011	0.0143	-0.0239	0.2025	0.1266	-0.0621	0.0112	0.1146	-0.1221	-0.0356	0	0.2472	-0.0293	-0.0197	0.2793	0.0392	0.2087	-16.3472	20.8408	-39.9801
20	0.0006	-0.0118	0.0103	0.0192	-0.0102	0.0061	-0.0231	0.1414	0.0946	-0.0569	0.0908	0.0703	-0.041	-0.098	0.0507	0.2905	-0.1794	-0.0429	0.2806	0.3284	0.1147	-52.5632	54.5348	-33.9497
21	0.0318	-0.0064	-0.0101	0.0138	-0.0067	0.0246	-0.0542	0.1682	-0.0541	-0.0821	0.053	0.007	-0.0527	0.0973	0.0118	0.1925	-0.0849	0.0157	0.2545	0.0112	0.1621	-44.8414	36.4759	-34.783
22	0.1933	0.079	0.0466	0.1829	0.0861	0.1239	-0.0534	0.1275	0.0018	-0.0357	0.0764	-0.0327	-0.0503	0.1096	0.1589	0.1452	-0.0579	-0.014	0.1871	0.0336	0.1579	-40.4136	39.8568	-19.5686
23	0.0138	-0.0229	0.0524	0.3246	-0.0097	0.2299	0.0176	-0.0096	0.1064	0.1817	0.1088	0.0387	-0.2632	0.0732	0.0944	0.3283	-0.0683	0.0074	0.1316	0.0149	0.2171	-40.6845	59.3238	-6.6216
24	-0.0016	0.0014	0.0092	0.0056	0.0086	0.045	0.0158	0.0404	0.103	0.0142	0.0451	0.0339	-0.0617	-0.0058	0.0424	0.4442	-0.0816	0.0096	0.1417	0.0755	0.3322	-42.3484	67.2487	-14.4752
25	0.1662	0.0014	-0.0634	0.0063	-0.0168	0.0675	-0.1078	0.2611	0.1391	-0.0046	0.0232	-0.0072	-0.1174	-0.0668	-0.0862	0.2581	-0.0711	-0.0065	0.336	0.1365	0.205	-65.0882	48.2008	-37.7413
26	0.0365	0.0122	-0.0089	0.0224	0.0262	0.0388	0.0302	0.0088	0.0818	0.0564	0.007	0.045	-0.0965	0.0042	0.017	0.1685	0.0074	0.0053	0.132	0.0525	0.1798	-69.3966	46.2664	-18.7407
27	0.0111	0.0038	0.0006	0.0034	-0.0012	0.0008	-0.0392	0.0605	-0.102	0.0218	-0.0001	-0.0289	0.0254	0.0022	0	0.1173	-0.0267	0.0019	0.1536	0.003	0.145	-66.9895	25.5247	-14.7537
28	0.0971	0.0524	0.0039	0.0293	-0.0106	0.0314	-0.0338	0.0971	0.0029	0.0628	0.0123	0.0514	-0.0225	-0.1239	0	0.1341	0.0038	0.016	0.1847	0.0179	0.1429	-79.9412	32.4906	-14.8683
29	0.0297	0.0026	-0.0228	0.0262	0.0074	0.0167	-0.0596	0.1006	0.219	0.0391	0.0466	0.0475	-0.089	-0.1242	-0.0001	0.2162	-0.0021	-0.0058	0.2008	0.0787	0.1886	-66.8785	45.2659	-23.1441
30	0.0194	0.0032	0.0123	0.0031	-0.0023	0.0257	-0.0012	0.3011	-0.041	-0.0867	0.0015	0.0692	0.0016	-0.0803	0.0072	0.1959	-0.0632	-0.0277	0.4396	-0.0131	0.1707	-81.0611	27.2424	-38.9944
31	0.0638	0.0703	0.0653	0.1044	0.0781	0.2	0.0791	0.3425	-0.1869	-0.0357	0.0125	-0.0441	0.0378	0.1162	0.0379	0.1928	-0.0014	0.0269	0.3969	-0.1076	0.1972	-70.1437	18.3859	-38.4286

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 35 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 36 through 54 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 55 through 83 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 84 through 156 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 157 through 218 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 219 through 242 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 243 through 272 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 273 through 292 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 293 through 313 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 314 through 349 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 350 through 375 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 7 through 35 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 36 through 72 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 73 through 103 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 104 through 156 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 157 through 181 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 182 through 272 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 273 through 313 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 314 through 375 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 21 through 54 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 55 through 89 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 90 through 292 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 293 through 349 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 350 through 375 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 23 through 56 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 57 through 103 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 104 through 127 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 128 through 218 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 219 through 272 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 273 through 313 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 314 through 375 )

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