PDB-5ojr: YCF48 bound to D1 peptide

ID or keywords:

Entry

Database: PDB / ID: 5ojr

Title

YCF48 bound to D1 peptide

Components

Photosystem II protein D1 3
Ycf48-like protein

Keywords

PHOTOSYNTHESIS / PHOTOSYSTEM II

Function / homology

Function and homology information

plasma membrane-derived thylakoid lumen / oxygen evolving activity / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / : ...
Similarity search - Function

Biological species

Thermosynechococcus elongatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.96 Å

Authors

Michoux, F. / Nixon, P.J. / Murray, J.W. / Bialek, W. / Thieulin-Pardo, G.

Funding support

United Kingdom, 1items

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Ycf48 involved in the biogenesis of the oxygen-evolving photosystem II complex is a seven-bladed beta-propeller protein.
Authors: Yu, J. / Knoppova, J. / Michoux, F. / Bialek, W. / Cota, E. / Shukla, M.K. / Straskova, A. / Pascual Aznar, G. / Sobotka, R. / Komenda, J. / Murray, J.W. / Nixon, P.J.

History

Deposition	Jul 23, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 8, 2018	Provider: repository / Type: Initial release
Revision 1.1	Aug 29, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 17, 2024	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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ojr.cif.gz	502 KB	Display	PDBx/mmCIF format
PDB format	pdb5ojr.ent.gz	414.5 KB	Display	PDB format
PDBx/mmJSON format	5ojr.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/oj/5ojr ftp://data.pdbj.org/pub/pdb/validation_reports/oj/5ojr	HTTPS FTP

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Related structure data

Related structure data	2xbgC 5oj3C 5oj5SC 5ojpC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3q30-d 3lee-3 6y7p-d 3vj9-d 3eu7-d 3lee-1 3wei-d 1td6-d 5o51-d 3weh-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) 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

Related structure data

2xbgC

5oj3C

5oj5SC

5ojpC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#59 - Nov 2004 Photosystem II similarity (7) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (6) #22 - Oct 2001 Photosystem I similarity (4)

Deposited unit

A: Ycf48-like protein

B: Ycf48-like protein

C: Ycf48-like protein

D: Ycf48-like protein

E: Photosystem II protein D1 3

F: Photosystem II protein D1 3

148 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ycf48-like protein

E: Photosystem II protein D1 3

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

2

B: Ycf48-like protein

F: Photosystem II protein D1 3

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

3

C: Ycf48-like protein

defined by author&software
36.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Ycf48-like protein

defined by author&software
36.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	97.320, 60.460, 103.460
Angle α, β, γ (deg.)	90.00, 96.78, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Ycf48-like protein Mass: 36195.535 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (bacteria) Gene: tll1695 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: Q8DI95
#2: Protein/peptide	Photosystem II protein D1 3 / PSII D1 protein 3 / Photosystem II Q(B) protein 3 Mass: 1824.964 Da / Num. of mol.: 2 / Fragment: UNP residues 335-352 / Source method: obtained synthetically / Source: (synth.) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIV4, photosystem II
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.04 Å³/Da / Density % sol: 39.6 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 20% v/v 2-Propanol, 20% w/v Polyethylene glycol 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.96→74.95 Å / Num. obs: 85525 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / CC_1/2: 0.995 / R_merge(I) obs: 0.14 / Net I/σ(I): 8.1
Reflection shell	Resolution: 1.96→1.99 Å / Redundancy: 3.5 % / R_merge(I) obs: 1.061 / Num. unique obs: 4040 / CC_1/2: 0.499 / % possible all: 95

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
xia2		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5OJ5

5oj5

Resolution: 1.96→74.945 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.56

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2381	4128	4.83 %	random
R_work	0.1929	-	-	-
obs	0.1951	85462	99.26 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.96→74.945 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9803	0	0	520	10323

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	10078
X-RAY DIFFRACTION	f_angle_d	1.109	13735
X-RAY DIFFRACTION	f_dihedral_angle_d	7.316	5854
X-RAY DIFFRACTION	f_chiral_restr	0.071	1455
X-RAY DIFFRACTION	f_plane_restr	0.008	1799

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 (%)
1.96-1.9831	0.2938	135	0.2837	2584	X-RAY DIFFRACTION	93
1.9831-2.0073	0.3167	152	0.2855	2771	X-RAY DIFFRACTION	99
2.0073-2.0327	0.3011	146	0.264	2800	X-RAY DIFFRACTION	100
2.0327-2.0594	0.3139	161	0.2599	2768	X-RAY DIFFRACTION	100
2.0594-2.0876	0.2834	143	0.2518	2788	X-RAY DIFFRACTION	99
2.0876-2.1175	0.3084	148	0.2512	2827	X-RAY DIFFRACTION	100
2.1175-2.1491	0.2986	141	0.2347	2795	X-RAY DIFFRACTION	100
2.1491-2.1827	0.2734	144	0.2338	2755	X-RAY DIFFRACTION	100
2.1827-2.2184	0.2736	152	0.2239	2837	X-RAY DIFFRACTION	100
2.2184-2.2567	0.2843	143	0.2297	2759	X-RAY DIFFRACTION	100
2.2567-2.2977	0.2619	139	0.2291	2818	X-RAY DIFFRACTION	100
2.2977-2.3419	0.3055	150	0.2229	2817	X-RAY DIFFRACTION	99
2.3419-2.3897	0.2686	142	0.2283	2788	X-RAY DIFFRACTION	100
2.3897-2.4417	0.3073	144	0.2194	2809	X-RAY DIFFRACTION	100
2.4417-2.4985	0.2971	150	0.2157	2784	X-RAY DIFFRACTION	99
2.4985-2.561	0.2539	117	0.2014	2817	X-RAY DIFFRACTION	100
2.561-2.6302	0.2547	125	0.1945	2853	X-RAY DIFFRACTION	100
2.6302-2.7076	0.2362	133	0.1972	2801	X-RAY DIFFRACTION	100
2.7076-2.795	0.2281	144	0.1966	2829	X-RAY DIFFRACTION	100
2.795-2.8949	0.2664	117	0.1967	2826	X-RAY DIFFRACTION	100
2.8949-3.0109	0.2438	152	0.1946	2806	X-RAY DIFFRACTION	99
3.0109-3.1479	0.2424	171	0.1943	2791	X-RAY DIFFRACTION	100
3.1479-3.3138	0.2717	149	0.1812	2803	X-RAY DIFFRACTION	99
3.3138-3.5215	0.1911	117	0.1779	2880	X-RAY DIFFRACTION	100
3.5215-3.7934	0.2208	126	0.1596	2829	X-RAY DIFFRACTION	99
3.7934-4.1751	0.1859	145	0.1512	2837	X-RAY DIFFRACTION	100
4.1751-4.7791	0.1557	152	0.1344	2822	X-RAY DIFFRACTION	99
4.7791-6.0208	0.1722	160	0.1556	2860	X-RAY DIFFRACTION	99
6.0208-75	0.2435	130	0.1894	2880	X-RAY DIFFRACTION	97

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	1.2311	0.6804	0.4614	0.9511	0.2912	0.5709	0.0354	-0.0608	0.0194	0.0878	0.0064	0.0167	0.0432	-0.048	-0.0313	0.2243	0.0378	-0.0193	0.1985	0.0044	0.1694	112.7161	-8.2705	10.2767
2	3.0009	1.718	0.1603	1.5374	0.2537	1.7748	-0.2112	0.429	0.4121	-0.2739	0.2455	0.149	0.0841	0.0834	-0.0368	0.2811	-0.028	-0.0582	0.3054	0.0475	0.2323	114.1269	-5.4708	-11.4762
3	4.6247	-0.1923	0.9513	6.1765	-0.6769	3.0332	0.0527	0.6515	0.2696	-0.4654	-0.0281	0.1684	0.1572	0.0199	0.0038	0.2348	-0.011	-0.0174	0.2953	0.0447	0.1707	102.9757	-14.565	-12.209
4	4.5631	0.2221	1.5106	2.9183	0.4744	4.6156	-0.1791	-0.2655	0.1718	0.0461	0.111	0.1416	-0.1856	-0.2892	0.0474	0.2001	0.0032	-0.0175	0.2065	-0.0019	0.185	97.5629	-18.166	2.9391
5	0.7122	-0.2327	0.2512	0.5814	0.1535	0.5394	0.028	0.0022	0.019	-0.0313	-0.0443	-0.0063	-0.0315	0.0077	0.0133	0.127	-0.0148	0.0073	0.1054	-0.0035	0.126	124.3453	-9.3674	46.5657
6	2.2889	0.3182	0.7354	4.7319	0.9451	3.1836	0.0987	-0.2843	0.0186	0.4281	-0.1268	-0.095	0.1088	0.031	0.0057	0.1302	-0.0076	0.0064	0.1589	0.0135	0.1338	135.2447	-16.915	62.1021
7	4.7981	-0.0853	1.145	3.007	-0.2814	3.4858	0.0056	0.1858	0.0743	-0.1248	-0.074	-0.1668	-0.0492	0.0925	0.039	0.1348	0.0065	0.0055	0.1299	-0.0085	0.1508	140.305	-18.7778	47.9065
8	4.0339	1.6239	2.3528	3.5222	2.1991	4.312	0.2775	-0.4986	-0.1172	0.5814	-0.2119	-0.1917	0.4255	-0.1837	0.1227	0.2383	0.0142	0.0102	0.2973	0.07	0.2378	136.9321	-36.813	20.5717
9	3.9475	0.6783	1.0507	2.3842	-0.3094	2.8862	0.2269	-0.2928	0.2094	0.2498	-0.2408	0.1552	0.1237	-0.1206	0.0506	0.2285	-0.0232	0.0416	0.1902	0.0087	0.1826	123.4422	-38.9893	9.5561
10	2.9804	0.2192	0.2628	4.1244	0.4092	2.9167	-0.1293	0.0758	-0.0296	-0.2766	0.099	0.2733	0.1208	0.1828	0.039	0.2026	-0.0145	-0.0221	0.1789	0.0428	0.2673	124.2558	-37.5597	-5.0523
11	5.1914	0.2688	1.8652	1.8027	0.4714	2.118	-0.1032	0.4848	0.3417	-0.1566	0.002	0.0238	-0.0453	0.2592	0.1157	0.2126	-0.0151	-0.0042	0.2068	0.0372	0.2104	130.3308	-25.4413	-8.021
12	1.6991	-0.1394	0.9106	1.9167	0.0071	4.0985	-0.1519	0.3012	0.2875	-0.1002	-0.0601	-0.2367	-0.1111	0.3439	0.2064	0.2077	0.0032	0.0143	0.2953	0.0568	0.2653	143.9104	-20.4312	-0.7952
13	2.0057	-1.6722	-0.6409	7.4211	0.6041	2.5467	0.0085	0.2044	0.8815	-0.0473	-0.2956	-0.0736	-0.3564	0.2274	0.2561	0.2367	-0.0258	-0.0584	0.3357	0.0294	0.4659	147.3311	-15.0876	6.1627
14	3.6834	2.4936	-1.7029	6.2999	0.8542	6.0213	0.0735	-0.2453	0.3729	0.3762	-0.1502	-0.2428	-0.0613	0.1934	0.0002	0.2271	0.0225	-0.0536	0.2506	0.0117	0.1877	143.616	-24.3547	15.318
15	4.072	0.8096	1.1917	3.8732	0.0093	3.2002	-0.033	-0.2098	-0.1911	0.0519	-0.0074	-0.1006	0.2373	0.0278	0.0382	0.2564	0.007	0.0387	0.2214	0.0154	0.1812	137.9551	-32.1416	17.7931
16	2.6184	-1.0165	0.7467	2.3976	-0.1763	2.7588	0.0911	0.2146	-0.0934	-0.2702	-0.1189	-0.0109	0.1062	0.0543	0.0169	0.1635	-0.0108	0.0307	0.1167	-0.0274	0.1263	108.8401	-39.4663	37.7613
17	2.4671	-0.6348	-0.0188	3.6655	0.3177	2.9455	-0.1451	-0.1342	-0.0529	0.2753	0.0936	-0.1318	0.0673	-0.0567	0.0773	0.1383	0.0077	0.0021	0.1315	-0.0235	0.1753	112.9093	-39.1815	56.4809
18	5.1007	-0.0442	2.2712	1.0291	-0.2599	1.6356	0.1191	-0.4488	-0.0024	0.1605	-0.0773	-0.0332	0.0543	-0.1691	0.023	0.16	-0.0039	0.0345	0.1451	-0.0231	0.1889	106.9297	-26.9708	59.4436
19	1.3182	-0.3742	0.9081	1.0612	-0.3186	3.7458	-0.0692	-0.2771	0.0965	0.0846	-0.0463	0.0784	-0.0398	-0.1553	0.1095	0.1701	0.0028	0.0316	0.2033	-0.0478	0.2235	93.2999	-21.8632	52.4782
20	5.0618	3.4695	-0.5148	2.5286	0.3185	4.0236	0.2493	-0.4782	0.7086	0.158	-0.3428	0.4461	-0.5	-0.2558	0.0819	0.2246	0.0369	0.0033	0.1967	-0.0418	0.3636	89.793	-16.4851	45.6119
21	2.0594	-2.0177	-0.8015	3.2374	-0.7437	5.3979	0.0714	0.0881	-0.0572	-0.2412	-0.0057	0.5315	-0.0368	-0.2997	-0.0038	0.1606	0.0065	-0.0479	0.1333	-0.0452	0.2154	92.5935	-25.8963	36.388
22	3.6776	-0.3742	0.8836	4.0073	-0.4468	3.211	-0.0378	0.1126	-0.0638	-0.2218	-0.0299	0.1768	0.0535	-0.1854	0.075	0.1771	0.0201	0.0382	0.1763	-0.0305	0.1555	99.0683	-33.2724	33.5581
23	2.8821	1.1039	1.3139	3.0054	0.2081	6.6193	-0.0327	0.132	0.2582	-0.1764	0.3432	-0.2846	-0.5642	-0.0477	-0.2175	0.2636	0.0267	-0.0313	0.3021	-0.0122	0.311	126.4212	3.9829	-5.4699
24	8.2434	3.2044	-5.9509	3.8188	-3.6968	5.0923	0.0317	-0.19	0.1347	0.4243	-0.3146	-0.3902	-0.2434	0.8803	0.29	0.4281	0.0426	-0.1015	0.3824	-0.0029	0.2765	126.485	0.3069	18.3351
25	7.9393	1.1757	4.7202	3.4139	1.3624	2.9744	-0.2793	-0.2697	0.4191	0.4223	0.0965	0.0174	-0.4084	-0.0142	0.15	0.2235	0.012	0.0108	0.203	-0.0246	0.1719	110.8241	2.4189	56.4735
26	5.7128	-0.3729	1.9624	7.2273	-0.4995	0.9105	-0.0209	0.2444	0.3507	-0.4738	-0.052	-0.307	-0.3452	0.2118	0.0499	0.3334	-0.0004	-0.0491	0.2744	0.0354	0.2682	105.3699	4.372	38.6186

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 31 through 177 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 178 through 226 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 227 through 277 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 278 through 341 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 30 through 226 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 227 through 287 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 288 through 340 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 38 through 57 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 58 through 91 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 92 through 149 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 150 through 200 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 201 through 242 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 243 through 259 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 260 through 287 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 288 through 340 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 38 through 91 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 92 through 149 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 150 through 200 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 201 through 242 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 243 through 259 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 260 through 287 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 288 through 340 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 335 through 344 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 345 through 352 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 335 through 344 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 345 through 351 )

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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

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Yorodumi