PDB-5ojp: YCF48 bound to D1 peptide

ID or keywords:

Entry

Database: PDB / ID: 5ojp

Title

YCF48 bound to D1 peptide

Components

Ycf48-like protein

Keywords

PHOTOSYNTHESIS / PHOTOSYSTEM II

Function / homology

Photosynthesis system II assembly factor Ycf48/Hcf136 / Photosynthesis system II assembly factor Ycf48/Hcf136-like domain / Photosynthesis system II assembly factor YCF48 / plasma membrane-derived thylakoid lumen / photosystem II / photosynthesis / WD40/YVTN repeat-like-containing domain superfamily / Photosystem II assembly protein Ycf48

Function and homology information

Biological species

Thermosynechococcus elongatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.86 Å

Authors

Michoux, F. / Nixon, P.J. / Murray, J.W.

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 22, 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	5ojp.cif.gz	370.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5ojp.ent.gz	304.8 KB	Display	PDB format
PDBx/mmJSON format	5ojp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ojp_validation.pdf.gz	453.4 KB	Display	wwPDB validaton report
Full document	5ojp_full_validation.pdf.gz	463.5 KB	Display
Data in XML	5ojp_validation.xml.gz	40.5 KB	Display
Data in CIF	5ojp_validation.cif.gz	54 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/5ojp ftp://data.pdbj.org/pub/pdb/validation_reports/oj/5ojp	HTTPS FTP

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Related structure data

Related structure data	2xbgSC 5oj3C 5oj5C 5ojrC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2xbg-d 5ojr-3 3tc3-1 4hzm-2 5ojr-4 5y9g-d 2w18-d 4zk8-d 4gvg-2 5utp-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) 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

2xbgSC

5oj3C

5oj5C

5ojrC

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 (1)

Deposited unit

A: Ycf48-like protein

B: Ycf48-like protein

C: Ycf48-like protein

108 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ycf48-like protein

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

2

B: Ycf48-like protein

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

3

C: Ycf48-like protein

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

Unit cell

Length a, b, c (Å)	54.441, 60.286, 75.398
Angle α, β, γ (deg.)	68.43, 74.83, 85.43
Int Tables number	1
Space group name H-M	P1

#1: Protein	Ycf48-like protein Mass: 36083.215 Da / Num. of mol.: 3 / Mutation: multi Arg to Glu variant Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (bacteria) Gene: tll1695 / Production host: Escherichia coli KRX / References: UniProt: Q8DI95
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.05 Å³/Da / Density % sol: 40.04 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: XX

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.21482 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.21482 Å / Relative weight: 1
Reflection	Resolution: 1.86→56.06 Å / Num. obs: 68907 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / CC_1/2: 0.997 / R_merge(I) obs: 0.056 / Net I/σ(I): 8.2
Reflection shell	Resolution: 1.86→1.91 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.81 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4141 / CC_1/2: 0.538 / % possible all: 77.5

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2xbg

2xbg

Resolution: 1.86→53.772 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.37

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2359	3001	5.02 %	random
R_work	0.1898	-	-	-
obs	0.1921	59833	82.76 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.86→53.772 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7101	0	0	230	7331

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	7300
X-RAY DIFFRACTION	f_angle_d	1.371	9953
X-RAY DIFFRACTION	f_dihedral_angle_d	7.355	4232
X-RAY DIFFRACTION	f_chiral_restr	0.086	1055
X-RAY DIFFRACTION	f_plane_restr	0.011	1303

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 (%)
1.86-1.8905	0.4913	54	0.425	993	X-RAY DIFFRACTION	30
1.8905-1.9231	0.4869	79	0.3983	1326	X-RAY DIFFRACTION	41
1.9231-1.9581	0.4585	78	0.3592	1695	X-RAY DIFFRACTION	52
1.9581-1.9957	0.3728	97	0.3421	1946	X-RAY DIFFRACTION	59
1.9957-2.0365	0.3802	104	0.2991	2126	X-RAY DIFFRACTION	64
2.0365-2.0808	0.3456	122	0.2951	2363	X-RAY DIFFRACTION	72
2.0808-2.1292	0.3259	141	0.2624	2465	X-RAY DIFFRACTION	77
2.1292-2.1824	0.3262	166	0.2602	2736	X-RAY DIFFRACTION	84
2.1824-2.2414	0.2547	167	0.2532	2934	X-RAY DIFFRACTION	91
2.2414-2.3074	0.2992	157	0.2458	3146	X-RAY DIFFRACTION	95
2.3074-2.3818	0.3139	186	0.2307	3108	X-RAY DIFFRACTION	96
2.3818-2.467	0.2691	169	0.2241	3137	X-RAY DIFFRACTION	96
2.467-2.5657	0.2632	160	0.2137	3177	X-RAY DIFFRACTION	97
2.5657-2.6825	0.2561	161	0.2197	3162	X-RAY DIFFRACTION	97
2.6825-2.8239	0.2823	155	0.2087	3186	X-RAY DIFFRACTION	97
2.8239-3.0009	0.2724	172	0.1995	3204	X-RAY DIFFRACTION	97
3.0009-3.2325	0.2354	156	0.1948	3203	X-RAY DIFFRACTION	98
3.2325-3.5578	0.222	170	0.1698	3221	X-RAY DIFFRACTION	98
3.5578-4.0724	0.1989	160	0.16	3220	X-RAY DIFFRACTION	99
4.0724-5.1302	0.184	177	0.1372	3229	X-RAY DIFFRACTION	99
5.1302-53.7948	0.18	170	0.1587	3255	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	0.1057	-0.1682	-0.2022	0.3612	0.0784	0.7243	-0.3526	-0.447	-0.4024	0.1975	0.2586	0.0596	-0.1789	-0.1838	0.0001	0.3615	0.0723	0.0549	0.5058	0.0785	0.3393	-41.9951	10.6024	14.9388
2	0.6601	-0.0389	0.1534	0.2475	-0.2722	0.4258	-0.1384	-0.4365	-0.2015	-0.0207	0.0296	-0.1227	0.256	0.1929	-0.0347	0.2969	0.0474	-0.0296	0.3772	0.0803	0.2983	-25.746	7.7936	8.9954
3	0.6738	-0.1537	-0.8715	0.2131	0.3019	1.1708	-0.0558	-0.2041	0.151	-0.0713	-0.078	-0.2489	0.025	0.3656	-0.184	0.2072	0.0193	-0.0384	0.3035	0.0298	0.3638	-19.0552	16.2075	-0.9469
4	0.5178	-0.0396	0.1059	0.4597	-0.0372	0.642	0.0561	-0.0414	0.1444	-0.257	-0.0243	-0.2888	-0.1435	0.0334	0.0014	0.2523	-0.0024	0.0204	0.2022	-0.0233	0.3388	-27.3837	17.831	-11.9987
5	1.1067	0.2206	0.3051	0.6416	-0.3339	0.3154	-0.0547	0.1865	0.1036	-0.1058	0.1433	0.0184	-0.2416	-0.2205	0.0036	0.26	0.0475	-0.0052	0.3105	-0.0247	0.1997	-42.6207	21.6429	-11.4042
6	1.121	0.3306	-0.2047	0.5847	-0.0787	0.5174	-0.1168	-0.0112	-0.0251	0.0893	0.1129	0.4218	-0.2362	-0.4607	-0.0007	0.2443	0.0358	-0.0201	0.4303	-0.0088	0.2894	-51.4099	14.9598	-0.1571
7	0.5008	-0.1375	0.4624	0.0973	-0.1791	0.4523	-0.212	-0.5901	-0.2779	0.1886	-0.0327	0.2556	-0.1455	-0.1412	-0.0017	0.3264	0.0565	-0.0156	0.4047	-0.02	0.3138	-40.3122	11.4521	9.9094
8	0.0812	-0.0782	-0.0119	0.0762	0.0479	0.4094	-0.2986	-0.3645	-0.1792	0.0407	0.2684	0.1478	-0.0197	-0.2466	0.0018	0.3307	-0.0367	0.0252	0.3876	0.093	0.2809	-40.7768	5.2005	12.8139
9	0.1617	-0.2214	-0.037	0.2977	-0.094	0.4656	0.0167	0.0094	-0.1332	-0.2679	-0.1045	-0.3579	0.509	0.0168	-0.0077	0.3372	0.0351	0.0227	0.2674	0.0652	0.5593	-14.0657	-20.3879	-11.8202
10	0.4106	-0.2888	0.0777	0.2934	-0.2941	0.3687	-0.0761	-0.3241	-0.3407	0.1482	0.1845	-0.1193	0.1762	-0.0008	0.0023	0.2865	-0.026	-0.021	0.2775	0.0494	0.2785	-30.5772	-16.4013	-7.849
11	0.7766	-0.6381	0.2851	0.6328	-0.6472	0.7682	0.1278	-0.0083	-0.2076	-0.2131	0.0388	0.3037	-0.0477	-0.1812	0.1023	0.2553	-0.0315	-0.0627	0.2479	0.0112	0.2881	-40.2342	-10.9681	-17.6979
12	0.1846	-0.0287	0.1602	0.2642	-0.0959	0.139	0.0229	0.0519	-0.0174	-0.3184	-0.0552	0.228	0.0595	-0.1936	0	0.2743	-0.0328	-0.036	0.3045	-0.0374	0.2434	-39.9871	0.4625	-20.295
13	0.5072	0.4399	-0.1589	0.3415	-0.1552	0.1918	0.0759	-0.08	0.0855	-0.3469	-0.0565	-0.1864	0.0895	-0.1071	-0.0276	0.4273	0.008	0.0918	0.2442	-0.0187	0.239	-29.2816	-0.3656	-27.4938
14	0.9749	0.0474	-0.168	0.5513	0.0995	0.092	0.2561	-0.0324	0.0596	-0.7746	-0.1047	-0.9142	0.1123	-0.1946	-0.1148	0.5152	0.2529	0.4282	-0.091	-0.189	0.3519	-20.1844	0.0741	-30.3025
15	0.9068	-0.755	1.2689	1.0322	-0.4447	2.7995	-0.132	0.0645	-0.313	0.1365	-0.4652	-0.3299	-0.4114	0.1282	-0.6444	0.5396	0.0263	0.3494	0.2492	-0.023	0.6467	-10.8463	1.9122	-28.7441
16	0.1193	-0.0794	-0.0521	0.049	-0.1402	0.5425	0.0447	0.0222	0.2195	-0.396	-0.1912	-0.766	0.415	0.165	-0.0628	0.3987	0.0519	0.1962	0.2458	0.0316	0.5901	-9.46	-8.8196	-20.5593
17	0.5919	-0.5855	-0.0276	1.1589	-0.2482	1.0955	-0.0115	-0.0352	-0.041	-0.4732	-0.1232	-0.5957	0.1995	0.0591	-0.024	0.2484	0.0167	0.0914	0.209	-0.0035	0.4357	-13.5944	-15.2832	-14.1058
18	1.1265	0.0541	-0.9093	0.3569	-0.3759	1.1032	-0.2165	0.3744	-0.0586	-0.075	-0.1225	0.3578	-0.8538	-0.8094	-0.2163	0.5768	0.0269	-0.2082	0.4132	-0.0551	0.5284	-62.7293	-15.2343	16.6315
19	0.2905	0.1771	0.2118	0.2504	0.2924	0.5414	-0.0834	0.0928	0.3101	0.4366	-0.2167	0.4586	-0.73	-0.1675	-0.014	0.6247	0.024	0.0566	0.3031	-0.0534	0.4233	-57.1839	-9.4696	32.3287
20	0.5006	-0.0203	-0.0337	0.3032	0.2681	0.244	0.0444	0.036	0.2976	-0.2652	0.0819	-0.004	-0.4254	0.1276	0.0075	0.76	-0.0946	-0.0125	0.3107	0.0151	0.3668	-45.609	-3.3092	33.8496
21	0.2471	-0.2189	0.0319	0.3013	0.075	0.0146	-0.0073	-0.0842	0.3779	0.2365	0.2138	-0.0209	0.0247	0.178	-0	0.6077	-0.1242	-0.1674	0.4877	-0.0363	0.3833	-40.5229	-4.8188	35.6501
22	1.6502	-0.8947	-0.6229	0.8362	1.1539	2.6446	0.2633	-0.2145	0.0681	0.1776	0.2308	-0.4975	-0.0117	0.5685	0.833	0.4539	-0.1448	-0.2264	0.5967	0.0712	0.3244	-34.8427	-12.1146	33.1805
23	0.0821	-0.1712	0.0089	0.2667	0.0385	0.0736	0.0118	0.4528	0.1545	-0.1038	-0.1626	-0.1958	0.1748	0.5134	-0.0003	0.4207	-0.033	-0.0663	0.8038	0.0783	0.5398	-33.402	-13.2089	29.2387
24	0.0176	0.0882	0.0606	0.2512	0.274	0.3046	-0.6241	0.0926	0.31	-0.4496	0.7175	-0.8221	-0.6986	0.2717	0.0025	0.4897	-0.073	0.0836	0.9543	-0.0778	0.6633	-31.0137	-17.3453	20.0345
25	0.0805	0.3063	-0.0451	1.19	-0.0571	0.0136	-0.0831	0.0082	0.2938	-0.8277	0.4007	-0.2698	-0.5167	0.7273	0.0544	0.4266	-0.0697	0.2281	0.7256	-0.1063	0.4839	-37.3367	-21.7856	13.038
26	0.2537	0.2278	0.1276	0.2361	0.0641	0.0647	-0.6674	0.9591	-0.3635	-0.1566	0.7935	-0.6236	0.2396	-0.4859	-0.0045	0.7964	-0.0167	0.2302	0.9265	-0.1441	0.696	-39.1872	-26.8377	8.9885
27	0.2364	0.0817	0.2571	0.2465	0.2705	0.3622	-0.2753	0.1459	-0.0254	-0.0989	0.1262	0.0545	0.1055	0.7463	-0.0006	0.4598	-0.0454	0.0524	0.3822	-0.0127	0.2456	-51.6574	-22.9846	12.1311
28	0.2533	-0.0493	-0.3286	0.0619	0.0039	0.5337	-0.7192	0.5712	0.2833	-0.3546	0.3897	0.1232	-0.2823	0.4866	-0.0615	0.4614	-0.0605	-0.1679	0.5417	0.0493	0.3494	-57.9709	-19.2788	10.611
29	0.4558	0.0448	-0.0814	0.1765	0.3465	0.5297	-0.4252	0.0709	0.3273	-0.0999	0.0859	0.1903	-0.0784	-0.3765	0.0003	0.484	-0.0018	-0.0037	0.3126	0.0059	0.3868	-58.3649	-16.8879	22.8496

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 38 through 57 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 91 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 92 through 149 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 150 through 200 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 201 through 242 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 243 through 305 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 306 through 329 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 330 through 346 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 38 through 57 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 58 through 91 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 92 through 149 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 150 through 174 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 175 through 200 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 201 through 242 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 243 through 259 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 260 through 287 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 288 through 341 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 38 through 57 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 58 through 91 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 92 through 124 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 125 through 149 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 150 through 167 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 168 through 195 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 196 through 216 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 217 through 242 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 243 through 261 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 262 through 287 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 288 through 316 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 317 through 341 )

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