PDB-6eys: Crystal structure of the periplasmic pyoverdine maturation protei...

ID or keywords:

Entry

Database: PDB / ID: 6eys

Title

Crystal structure of the periplasmic pyoverdine maturation protein PvdP

Components

PvdP

Keywords

OXIDOREDUCTASE / pyoverdine / tyrosinase / barrel / multidomain

Function / homology

Di-copper centre-containing domain superfamily / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / PvdP

Function and homology information

Biological species

Pseudomonas aeruginosa UCBPP-PA14 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.091 Å

Authors

Poppe, J. / Blankenfeldt, W.

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Pseudomonas aeruginosapyoverdine maturation enzyme PvdP has a noncanonical domain architecture and affords insight into a new subclass of tyrosinases.
Authors: Poppe, J. / Reichelt, J. / Blankenfeldt, W.

History

Deposition	Nov 13, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 1, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 3, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6eys.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb6eys.ent.gz	916.5 KB	Display	PDB format
PDBx/mmJSON format	6eys.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6eys_validation.pdf.gz	454.2 KB	Display	wwPDB validaton report
Full document	6eys_full_validation.pdf.gz	459.9 KB	Display
Data in XML	6eys_validation.xml.gz	65.4 KB	Display
Data in CIF	6eys_validation.cif.gz	91.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ey/6eys ftp://data.pdbj.org/pub/pdb/validation_reports/ey/6eys	HTTPS FTP

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Related structure data

Related structure data	6eyvC C: citing same article (ref.)
Similar structure data	6rrr-d 6rrq-d 6rrp-d 6eyv-d 6d9d-1 5wg6-1 4mo2-d 5vn5-d 6d9a-1 4rph-1 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (1)

Deposited unit

B: PvdP

A: PvdP

C: PvdP

D: PvdP

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

1

B: PvdP

A: PvdP

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

2

C: PvdP

D: PvdP

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

Unit cell

Length a, b, c (Å)	97.353, 107.793, 107.945
Angle α, β, γ (deg.)	90.00, 99.97, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	PvdP Mass: 61758.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria) Strain: UCBPP-PA14 / Gene: pvdP, PA14_33740 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: A0A0H2ZBG1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.26 Å³/Da / Density % sol: 45.53 % / Description: thin plates
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20%PEG3350 0.18M tri-Ammoniumcitrat

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9794 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 26, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.091→48.072 Å / Num. obs: 85942 / % possible obs: 93.2 % / Redundancy: 6.7 % / CC_1/2: 0.997 / R_pim(I) all: 0.051 / Net I/σ(I): 10.7
Reflection shell	Resolution: 2.091→2.259 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4285 / CC_1/2: 0.537 / R_pim(I) all: 0.499 / % possible all: 76.7

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2875)	refinement
XDS		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.091→45.606 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.27

	R_factor	Num. reflection	% reflection
R_free	0.241	1999	2.33 %
R_work	0.2141	-	-
obs	0.2147	85903	93.2 %

Solvent computation

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

Displacement parameters

B_iso mean: 47 Å²

Refinement step

Cycle: LAST / Resolution: 2.091→45.606 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15214	0	0	513	15727

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	15760
X-RAY DIFFRACTION	f_angle_d	0.495	21456
X-RAY DIFFRACTION	f_dihedral_angle_d	13.989	9208
X-RAY DIFFRACTION	f_chiral_restr	0.04	2158
X-RAY DIFFRACTION	f_plane_restr	0.003	2834

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 (%)
2.0909-2.1431	0.4321	12	0.321	535	X-RAY DIFFRACTION	6
2.1431-2.2011	0.3431	39	0.3225	1615	X-RAY DIFFRACTION	18
2.2011-2.2659	0.4021	55	0.3061	2301	X-RAY DIFFRACTION	26
2.2659-2.339	0.344	74	0.3041	3127	X-RAY DIFFRACTION	35
2.339-2.4226	0.3524	91	0.2953	3801	X-RAY DIFFRACTION	42
2.4226-2.5196	0.3332	114	0.3003	4751	X-RAY DIFFRACTION	53
2.5196-2.6342	0.3189	139	0.2783	5852	X-RAY DIFFRACTION	64
2.6342-2.7731	0.2866	180	0.2685	7569	X-RAY DIFFRACTION	84
2.7731-2.9468	0.3034	216	0.2711	9018	X-RAY DIFFRACTION	100
2.9468-3.1743	0.2964	215	0.2434	9038	X-RAY DIFFRACTION	100
3.1743-3.4936	0.2344	216	0.2192	9045	X-RAY DIFFRACTION	100
3.4936-3.9989	0.2031	215	0.181	9043	X-RAY DIFFRACTION	100
3.9989-5.0372	0.1909	217	0.1618	9090	X-RAY DIFFRACTION	100
5.0372-45.6166	0.2122	216	0.1924	9119	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	1.7328	0.9192	0.231	2.6942	-0.1678	2.1848	-0.1506	0.0533	0.0612	-0.2719	0.1753	0.39	0.1826	-0.2148	-0.0252	0.2363	-0.0174	-0.0344	0.1656	0.0484	0.3329	-6.1349	-3.8633	-27.4111
2	0.8336	0.4216	-0.4388	1.0371	-0.4349	1.1517	-0.0309	0.1504	-0.0276	-0.1738	0.0158	0.0562	0.0995	-0.0306	0.0158	0.2382	0.0215	-0.0614	0.2095	0.0001	0.2732	3.5236	16.1133	-49.6855
3	1.2941	-0.0467	-0.2698	2.5383	0.0202	1.7954	-0.0676	0.2159	-0.0888	-0.3345	0.1031	0.0311	0.1205	0.0067	-0.0227	0.2768	-0.0335	-0.0513	0.2495	0.0387	0.2734	7.5839	23.4434	-55.2071
4	2.2385	-0.9066	-0.7449	2.3399	-0.2054	1.8761	-0.0068	0.1033	-0.0052	0.1631	0.0967	0.324	-0.2915	-0.273	-0.0634	0.2769	0.0349	0.0109	0.192	0.0492	0.3491	-6.3082	35.199	-29.7219
5	0.4032	-0.5877	0.4069	1.851	-0.6171	1.3432	-0.0747	-0.1424	-0.0078	0.5825	0.0819	0.2308	-0.135	-0.1154	0.0051	0.4178	0.0053	0.125	0.2828	0.0088	0.296	-5.7703	15.4767	-3.2162
6	2.0216	-0.2507	0.2049	0.7294	-0.1654	2.0428	-0.0211	-0.0578	0.1567	0.3328	0.0588	0.143	-0.1766	-0.0112	-0.0234	0.3313	0.0015	0.0508	0.1751	0.0067	0.2673	0.6127	10.7864	-9.4879
7	1.4013	0.0318	0.1368	1.7459	-0.0328	2.1092	-0.029	-0.3449	0.0852	0.7067	0.0212	0.2952	-0.1489	-0.0662	0.0176	0.5058	0.0151	0.0966	0.2946	0.0332	0.2758	-3.1449	7.2014	3.073
8	2.4479	1.42	-0.4916	2.608	0.1043	2.9332	-0.0293	0.0509	-0.1617	0.2428	0.0153	-0.13	0.1831	0.2718	0.0148	0.1776	0.0614	0.0149	0.2623	-0.0007	0.1432	48.9708	24.4821	-11.5789
9	1.9145	0.364	-0.5333	1.8906	0.0877	3.4759	-0.055	0.2076	0.0027	0.2493	-0.0642	0.4555	0.0279	-0.6478	0.1121	0.2212	0.0176	0.055	0.3594	-0.053	0.217	34.2203	25.6076	-10.3611
10	2.4986	1.0253	0.8579	3.0071	-0.7684	4.1306	0.0152	-0.3276	-0.0004	0.3055	0.2257	-0.112	0.241	-0.3084	-0.2092	0.4539	0.0108	0.0736	0.4613	-0.0501	0.1765	38.7126	22.7261	-2.0532
11	0.6123	-0.7308	-0.8663	1.4444	1.2211	2.0669	-0.2541	-0.1553	0.0141	0.6044	0.3011	-0.1171	0.7797	0.2268	-0.0302	0.5237	0.0551	-0.0166	0.2719	-0.0254	0.2247	50.7151	-4.5259	-25.1527
12	0.8345	-0.7469	-0.8506	1.7892	0.9957	2.0763	0.019	-0.0031	-0.1215	0.0978	-0.078	0.1197	0.1435	-0.1063	0.0549	0.2675	-0.029	-0.0146	0.3474	-0.0018	0.2089	45.3677	6.3094	-30.6355
13	1.6705	-0.6714	0.2829	1.5774	0.7625	1.9817	-0.0223	-0.2393	-0.2178	0.4719	-0.0421	0.036	0.209	0.2996	0.0764	0.4469	0.024	-0.034	0.3487	-0.0016	0.2393	52.8984	-0.3718	-31.6148
14	1.6953	-0.3711	0.1015	2.6285	0.1108	2.5088	-0.0798	0.0039	-0.3216	0.1248	0.0541	0.0749	0.6707	-0.1968	0.0037	0.3819	-0.0409	0.0054	0.2954	-0.0477	0.2914	48.5102	-6.2206	-41.7034
15	1.77	-0.6169	0.1553	2.6612	-0.0599	2.8062	-0.1965	-0.2576	-0.2749	0.6189	0.1291	-0.0837	0.9634	0.472	0.0632	0.7166	0.202	-0.0206	0.4765	0.0512	0.3581	59.6366	-9.8643	-26.7477
16	0.7281	-0.0158	0.8006	1.8748	0.0043	4.2084	0.0181	-0.0729	-0.042	-0.1014	0.0655	-0.3059	-0.421	0.0419	-0.0944	0.1277	-0.0247	0.0327	0.2997	-0.0244	0.2098	54.3239	22.255	-41.9838
17	0.8921	-0.0129	-0.5465	1.465	0.4148	0.4483	0.0459	-0.0846	0.0502	-0.5197	-0.0857	0.0582	-0.6083	-0.6006	0.0123	0.3046	0.1829	-0.0732	0.4726	-0.0637	0.1561	39.2501	24.6181	-49.0706
18	2.9147	-0.1616	-0.8598	3.0228	-0.9699	1.0013	-0.0144	-0.101	-0.0439	-0.4464	-0.1647	0.1691	-0.1608	-0.5006	0.0948	0.2477	0.0933	-0.0447	0.4331	-0.0844	0.1532	45.143	20.6249	-50.3947
19	0.3509	0.2967	0.1416	2.1995	-0.0614	0.5618	0.0157	0.1485	0.0031	-0.4008	0.0476	-0.0031	-0.659	-0.2185	-0.0795	0.5232	0.1179	-0.0245	0.4593	0.0325	0.2087	42.1806	38.4012	-46.7614
20	4.1758	1.1132	0.5419	2.5577	0.8657	4.1433	-0.0486	0.1271	0.086	-0.0516	0.0948	0.1386	-0.5629	0.1528	-0.0027	0.9942	-0.1459	0.0005	0.3684	0.0061	0.2809	59.7091	62.2335	-19.0792
21	0.7042	0.5234	0.396	1.4595	0.9286	1.8868	0.0344	-0.0846	0.2544	0.1701	-0.0826	0.0288	-0.711	-0.1063	0.0366	0.7035	0.088	-0.0035	0.3886	-0.0451	0.2169	46.93	50.9175	-16.9298
22	0.7607	0.0993	0.4888	0.8207	0.5365	3.5463	0.1187	-0.0264	-0.005	-0.0629	-0.0281	-0.031	-0.1574	-0.0381	-0.0884	0.3188	0.0637	0.0345	0.26	-0.016	0.187	48.4609	36.0012	-28.568
23	2.5479	0.0884	-0.0858	1.8583	0.3432	0.0673	-0.032	0.2456	0.1347	-0.1753	-0.04	-0.1538	-0.2564	0.1955	0.0738	0.5143	-0.0068	0.0195	0.3284	-0.0109	0.2146	50.0695	45.2281	-19.4398
24	1.8206	0.4558	-0.1666	1.8622	-1.0027	3.7025	-0.0979	0.2859	0.2757	-0.1513	-0.0225	0.0433	-0.9014	-0.0655	0.0824	0.6551	0.0329	-0.0469	0.2902	-0.0389	0.2595	47.4205	51.7285	-24.1839
25	0.4753	0.3373	0.1431	0.7154	-0.4992	0.7923	0.1275	-0.2729	0.2512	0.3462	-0.0426	0.1897	-0.7844	-0.11	0.392	1.1405	0.0589	0.0321	0.4894	-0.1048	0.3082	44.9093	58.1455	-3.9407
26	2.7217	-1.2351	-0.2036	4.5123	0.5918	2.9507	0.0303	0.0365	0.3523	0.2896	0.0517	-0.4049	-1.0423	0.1389	-0.0745	0.6502	-0.0846	-0.0219	0.4706	0.0154	0.3377	61.9817	53.3922	-25.6796

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 36 through 169 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 170 through 353 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 354 through 542 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 36 through 169 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 170 through 319 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 320 through 391 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 392 through 541 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 36 through 67 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 68 through 139 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 140 through 169 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 170 through 262 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 263 through 353 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 354 through 404 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 405 through 479 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 480 through 541 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 36 through 67 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 68 through 105 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 106 through 169 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 170 through 209 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 210 through 240 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 241 through 300 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 301 through 353 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 354 through 391 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 392 through 449 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 450 through 500 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 501 through 541 )

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