6JLM

XFEL structure of cyanobacterial photosystem II (dark state, dataset2)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, U (A, a)	Photosystem II protein D1	polymer	344	38235.6	2	UniProt (P51765) Pfam (PF00124)	Thermosynechococcus vulcanus	PSII D1 protein,Photosystem II Q(B) protein
2	B, V (B, b)	Photosystem II CP47 reaction center protein	polymer	505	56068.7	2	UniProt (D0VWR1) Pfam (PF00421)	Thermosynechococcus vulcanus	PSII 47 kDa protein,Protein CP-47
3	C, W (C, c)	Photosystem II CP43 reaction center protein	polymer	455	49668.8	2	UniProt (D0VWR7) Pfam (PF00421)	Thermosynechococcus vulcanus	PSII 43 kDa protein,Protein CP-43
4	D, X (D, d)	Photosystem II D2 protein	polymer	342	38404.9	2	UniProt (D0VWR8) Pfam (PF00124)	Thermosynechococcus vulcanus	PSII D2 protein,Photosystem Q(A) protein
5	E, Y (E, e)	Cytochrome b559 subunit alpha	polymer	84	9580.8	2	UniProt (P12238) Pfam (PF00283) Pfam (PF00284)	Thermosynechococcus vulcanus	PSII reaction center subunit V
6	F, Z (F, f)	Cytochrome b559 subunit beta	polymer	44	4936.7	2	UniProt (P12239) Pfam (PF00283)	Thermosynechococcus vulcanus	PSII reaction center subunit VI
7	AA, G (H, h)	Photosystem II reaction center protein H	polymer	65	7227.6	2	UniProt (P19052) Pfam (PF00737)	Thermosynechococcus vulcanus	PSII-H
8	BA, H (I, i)	Photosystem II reaction center protein I	polymer	38	4438.3	2	UniProt (P12240) Pfam (PF02532)	Thermosynechococcus vulcanus (Synechococcus vulcanus)	PSII-I,PSII 4.4 kDa protein
9	CA, I (J, j)	Photosystem II reaction center protein J	polymer	39	3974.7	2	UniProt (Q7DGD4) Pfam (PF01788)	Thermosynechococcus vulcanus	PSII-J
10	DA, J (K, k)	Photosystem II reaction center protein K	polymer	37	4101.9	2	UniProt (P19054) Pfam (PF02533)	Thermosynechococcus vulcanus	PSII-K
11	EA, K (L, l)	Photosystem II reaction center protein L	polymer	37	4299.0	2	UniProt (P12241) Pfam (PF02419)	Thermosynechococcus vulcanus	PSII-L
12	FA, L (M, m)	Photosystem II reaction center protein M	polymer	36	4009.7	2	UniProt (P12312) Pfam (PF05151)	Thermosynechococcus vulcanus (Synechococcus vulcanus)	PSII-M
13	GA, M (O, o)	Photosystem II manganese-stabilizing polypeptide	polymer	244	26651.7	2	UniProt (D0VWR2) Pfam (PF01716)	Thermosynechococcus vulcanus	MSP
14	HA, N (T, t)	Photosystem II reaction center protein T	polymer	32	3906.7	2	UniProt (P12313) Pfam (PF01405)	Thermosynechococcus vulcanus (Synechococcus vulcanus)	PSII-Tc
15	IA, O (U, u)	Photosystem II 12 kDa extrinsic protein	polymer	104	11656.0	2	UniProt (P56152) Pfam (PF06514)	Thermosynechococcus vulcanus	PS II complex 12 kDa extrinsic protein,PSII-U
16	JA, P (V, v)	Cytochrome c-550	polymer	137	15148.3	2	UniProt (P0A387) Pfam (PF14495)	Thermosynechococcus vulcanus	Cytochrome c550,Low-potential cytochrome c
17	KA, Q (Y, y)	Photosystem II reaction center protein Ycf12	polymer	30	3228.0	2	UniProt (D0VWR3) Pfam (PF05969)	Thermosynechococcus vulcanus
18	LA, R (X, x)	Photosystem II reaction center protein X	polymer	40	4191.0	2	UniProt (D0VWR4) Pfam (PF06596)	Thermosynechococcus vulcanus
19	MA, S (Z, z)	Photosystem II reaction center protein Z	polymer	62	6766.2	2	UniProt (D0VWR5) Pfam (PF01737)	Thermosynechococcus vulcanus	PSII-Z
20	T (R)	Photosystem II protein Y	polymer	34	3859.7	1	UniProt (P0DM37) Pfam (PF06298)	Thermosynechococcus vulcanus
21	NA, PI (A, d)	FE (II) ION	non-polymer		55.8	2	Chemie (FE2)
22	NF, OA, OF, PA, WJ... (a, A, v, U)	CHLORIDE ION	non-polymer		35.5	6	Chemie (CL)
23	QA, QI (A, d)	BICARBONATE ION	non-polymer		61.0	2	Chemie (BCT)
24	AD, AI, BD, CD, HB... (C, c, B, b, a...)	CHLOROPHYLL A	non-polymer		893.5	70	Chemie (CLA)
25	QD, RF, RI, UA (D, a, d, A)	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
26	AH, BH, BI, BK, DD... (b, c, y, C, H...)	BETA-CAROTENE	non-polymer		536.9	22	Chemie (BCR)
27	AB, AC, GE, HJ, MF... (A, B, F, f, a...)	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	non-polymer		795.1	8	Chemie (SQD)
28	AF, AK, DF, DG, EF... (V, v, a, B, b...)	GLYCEROL	non-polymer		92.1	35	Chemie (GOL)
29	BB, BG, DH, EE, FG... (A, a, b, F, e...)	DODECYL-BETA-D-MALTOSIDE	non-polymer		510.6	14	Chemie (LMT)
30	AG, CB (a, A)	CA-MN4-O5 CLUSTER	non-polymer		339.8	2	Chemie (OEX)
31	DB, WD, WI, ZF (A, D, d, a)	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)
32	AE, AJ, BE, BJ, CK... (D, d, x, A, X...)	UNKNOWN LIGAND	non-polymer		749.2	18	Chemie (UNL)
33	BC, CH, DJ, DK, FB... (B, b, d, z, A...)	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	12	Chemie (LMG)
34	GB, HE, IG, IJ, MI... (B, F, b, f, c...)	CALCIUM ION	non-polymer		40.1	9	Chemie (CA)
35	CC, CE, CF, CJ, DC... (B, D, V, d, b...)	heptyl 1-thio-beta-D-glucopyranoside	non-polymer		294.4	17	Chemie (HTG)
36	CG, DE, MH, OC, PE... (a, E, b, B, L...)	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	10	Chemie (LHG)
37	CI, DI, EI, EJ, FD... (c, e, C, H, h...)	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	10	Chemie (DGD)
38	BF, FE, GJ, XJ (V, F, f, v)	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	4	Chemie (HEM)
39	NE, NJ (J, j)	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG)
40	AL, BL, CL, DL, EK... (d, e, f, h, A...)	water	water		18.0	2585	Chemie (HOH)

Sequence modifications

A, a: 1 - 344 (UniProt: P51765)

PDB	External Database	Details
Pro 279	Arg 279	See sequence details

C, c: 23 - 473 (UniProt: D0VWR7)

PDB	External Database	Details
Asn 19	-	See sequence details
Ser 20	-	See sequence details
Ile 21	-	See sequence details
Phe 22	-	See sequence details

K, k: 10 - 46 (UniProt: P19054)

PDB	External Database	Details
Leu 33	Phe 24	See sequence details
Trp 39	Val 30	See sequence details

M, m: 1 - 36 (UniProt: P12312)

PDB	External Database	Details
Leu 8	Phe 8	See sequence details

Contents of the asymmetric unit

Polymers	Number of chains	39
	Total formula weight	596849.1
Non-Polymers*	Number of molecules	251
	Total formula weight	146230.4
All*	Total formula weight	743079.5

*Water molecules are not included.