5GTH

Native XFEL structure of photosystem II (dark dataset)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, a	Photosystem II protein D1	polymer	344	38235.6	2	Pfam (PF00124) UniProt (by SIFTS) (P51765) In PDB	Thermosynechococcus vulcanus
2	B, b	Photosystem II CP47 reaction center protein	polymer	505	56068.7	2	UniProt (D0VWR1) Pfam (PF00421) In PDB	Thermosynechococcus vulcanus	PSII 47 kDa protein,Protein CP-47
3	C, c	Photosystem II CP43 reaction center protein	polymer	455	49668.8	2	Pfam (PF00421) UniProt (by SIFTS) (D0VWR7) In PDB	Thermosynechococcus vulcanus
4	D, d	Photosystem II D2 protein	polymer	342	38404.9	2	UniProt (D0VWR8) Pfam (PF00124) In PDB	Thermosynechococcus vulcanus	PSII D2 protein,Photosystem Q(A) protein
5	E, e	Cytochrome b559 subunit alpha	polymer	84	9580.8	2	UniProt (P12238) Pfam (PF00283) Pfam (PF00284) In PDB	Thermosynechococcus vulcanus	PSII reaction center subunit V
6	F, f	Cytochrome b559 subunit beta	polymer	44	4936.7	2	UniProt (P12239) Pfam (PF00283) In PDB	Thermosynechococcus vulcanus	PSII reaction center subunit VI
7	H, h	Photosystem II reaction center protein H	polymer	65	7227.6	2	UniProt (P19052) Pfam (PF00737) In PDB	Thermosynechococcus vulcanus	PSII-H
8	I, i	Photosystem II reaction center protein I	polymer	38	4438.3	2	UniProt (P12240) Pfam (PF02532) In PDB	Thermosynechococcus vulcanus	PSII-I,PSII 4.4 kDa protein
9	J, j	Photosystem II reaction center protein J	polymer	39	3974.7	2	UniProt (Q7DGD4) Pfam (PF01788) In PDB	Thermosynechococcus vulcanus	PSII-J
10	K, k	Photosystem II reaction center protein K	polymer	37	4101.9	2	Pfam (PF02533) UniProt (by SIFTS) (P19054) In PDB	Thermosynechococcus vulcanus	PSII-K
11	L, l	Photosystem II reaction center protein L	polymer	37	4299.0	2	UniProt (P12241) Pfam (PF02419) In PDB	Thermosynechococcus vulcanus	PSII-L
12	M, m	Photosystem II reaction center protein M	polymer	36	4009.7	2	Pfam (PF05151) UniProt (by SIFTS) (P12312) In PDB	Thermosynechococcus vulcanus	PSII-M
13	O, o	Photosystem II manganese-stabilizing polypeptide	polymer	244	26651.7	2	UniProt (D0VWR2) Pfam (PF01716) In PDB	Thermosynechococcus vulcanus	MSP
14	T, t	Photosystem II reaction center protein T	polymer	32	3906.7	2	UniProt (P12313) Pfam (PF01405) In PDB	Thermosynechococcus vulcanus	PSII-Tc
15	U, u	Photosystem II 12 kDa extrinsic protein	polymer	104	11656.0	2	UniProt (P56152) Pfam (PF06514) In PDB	Thermosynechococcus vulcanus	PS II complex 12 kDa extrinsic protein,PSII-U
16	V, v	Cytochrome c-550	polymer	137	15148.3	2	UniProt (P0A387) Pfam (PF14495) In PDB	Thermosynechococcus vulcanus	Cytochrome c550,Low-potential cytochrome c
17	X, x	Photosystem II reaction center protein X	polymer	40	4191.0	2	UniProt (D0VWR4) Pfam (PF06596) In PDB	Thermosynechococcus vulcanus
18	Y, y	Photosystem II reaction center protein Ycf12	polymer	30	3228.0	2	UniProt (D0VWR3) Pfam (PF05969) In PDB	Thermosynechococcus vulcanus
19	Z, z	Photosystem II reaction center protein Z	polymer	62	6766.2	2	UniProt (D0VWR5) Pfam (PF01737) In PDB	Thermosynechococcus vulcanus	PSII-Z
20	R	Photosystem II protein Y	polymer	34	3859.7	1	UniProt (P0DM37) Pfam (PF06298) In PDB	Thermosynechococcus vulcanus
21	A, a	FE (II) ION	non-polymer		55.8	2	Chemie (FE2)
22	A, a	CHLORIDE ION	non-polymer		35.5	4	Chemie (CL)
23	b, c, a, B, C...	CHLOROPHYLL A	non-polymer		893.5	70	Chemie (CLA)
24	a, D, A	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
25	a, b, c, h, K...	BETA-CAROTENE	non-polymer		536.9	22	Chemie (BCR)
26	f, a, L, D, A...	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	non-polymer		795.1	8	Chemie (SQD)
27	B, a, C, b, d...	GLYCEROL	non-polymer		92.1	7	Chemie (GOL)
28	a, A	CA-MN4-O5 CLUSTER	non-polymer		339.8	2	Chemie (OEX)
29	A, a, D, d	2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE	non-polymer		749.2	4	Chemie (PL9)
30	A, I, J, K, i...	UNKNOWN LIGAND	non-polymer		568.9	18	Chemie (UNL)
31	A, l, D, d, E...	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	10	Chemie (LHG)
32	A, a	BICARBONATE ION	non-polymer		61.0	2	Chemie (BCT)
33	J, C, b, j, c...	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	12	Chemie (LMG)
34	B, C, b, c, V...	heptyl 1-thio-beta-D-glucopyranoside	non-polymer		294.4	15	Chemie (HTG)
35	I, e, b, B, M...	DODECYL-BETA-D-MALTOSIDE	non-polymer		510.6	14	Chemie (LMT)
36	C, c, h, H	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	8	Chemie (DGD)
37	C, O, c, V, o	CALCIUM ION	non-polymer		40.1	6	Chemie (CA)
38	e, E	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	2	Chemie (HEM)
39	J, j	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG)
40	V, v	HEME C	non-polymer		618.5	2	Chemie (HEC)
41		water	water		18.0	1781	Chemie (HOH)

Contents of the asymmetric unit

Polymers	Number of chains	39
	Total formula weight	596849.1
Non-Polymers*	Number of molecules	214
	Total formula weight	137732.0
All*	Total formula weight	734581.1

*Water molecules are not included.