5KAF

RT XFEL structure of Photosystem II in the dark state at 3.0 A resolution

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 1	polymer	344	38265.6	2	UniProt (P0A444) Pfam (PF00124)	Thermosynechococcus elongatus (strain BP-1)	PSII D1 protein 1,Photosystem II Q(B) protein 1
2	B, V (B, b)	Photosystem II CP47 reaction center protein	polymer	510	56656.5	2	UniProt (Q8DIQ1) Pfam (PF00421)	Thermosynechococcus elongatus (strain BP-1)	PSII 47 kDa protein,Protein CP-47
3	C, W (C, c)	Photosystem II CP43 reaction center protein	polymer	461	50287.5	2	UniProt (Q8DIF8) Pfam (PF00421)	Thermosynechococcus elongatus (strain BP-1)	PSII 43 kDa protein,Protein CP-43
4	D, X (D, d)	Photosystem II D2 protein	polymer	352	39388.2	2	UniProt (Q8CM25) Pfam (PF00124)	Thermosynechococcus elongatus (strain BP-1)	PSII D2 protein,Photosystem II Q(A) protein
5	E, Y (E, e)	Cytochrome b559 subunit alpha	polymer	84	9580.8	2	UniProt (Q8DIP0) Pfam (PF00283) Pfam (PF00284)	Thermosynechococcus elongatus (strain BP-1)	PSII reaction center subunit V
6	F, Z (F, f)	Cytochrome b559 subunit beta	polymer	45	5067.9	2	UniProt (Q8DIN9) Pfam (PF00283)	Thermosynechococcus elongatus (strain BP-1)	PSII reaction center subunit VI
7	AA, G (H, h)	Photosystem II reaction center protein H	polymer	66	7358.8	2	UniProt (Q8DJ43) Pfam (PF00737)	Thermosynechococcus elongatus (strain BP-1)	PSII-H
8	BA, H (I, i)	Photosystem II reaction center protein I	polymer	38	4438.3	2	UniProt (Q8DJZ6) Pfam (PF02532)	Thermosynechococcus elongatus (strain BP-1)	PSII-I,PSII 4.4 kDa protein
9	CA, I (J, j)	Photosystem II reaction center protein J	polymer	40	4105.9	2	UniProt (P59087) Pfam (PF01788)	Thermosynechococcus elongatus (strain BP-1)	PSII-J
10	DA, J (K, k)	Photosystem II reaction center protein K	polymer	46	5028.1	2	UniProt (Q9F1K9) Pfam (PF02533)	Thermosynechococcus elongatus (strain BP-1)	PSII-K
11	EA, K (L, l)	Photosystem II reaction center protein L	polymer	37	4299.0	2	UniProt (Q8DIN8) Pfam (PF02419)	Thermosynechococcus elongatus (strain BP-1)	PSII-L
12	FA, L (M, m)	Photosystem II reaction center protein M	polymer	36	4009.7	2	UniProt (Q8DHA7) Pfam (PF05151)	Thermosynechococcus elongatus (strain BP-1)	PSII-M
13	GA, M (O, o)	Photosystem II manganese-stabilizing polypeptide	polymer	272	29637.4	2	UniProt (P0A431) Pfam (PF01716)	Thermosynechococcus elongatus (strain BP-1)	MSP
14	HA, N (T, t)	Photosystem II reaction center protein T	polymer	32	3906.7	2	UniProt (Q8DIQ0) Pfam (PF01405)	Thermosynechococcus elongatus (strain BP-1)	PSII-Tc
15	IA, O (U, u)	Photosystem II 12 kDa extrinsic protein	polymer	134	15031.0	2	UniProt (Q9F1L5) Pfam (PF06514)	Thermosynechococcus elongatus (strain BP-1)	PS II complex 12 kDa extrinsic protein,PSII-U
16	JA, P (V, v)	Cytochrome c-550	polymer	163	18046.9	2	UniProt (P0A386) Pfam (PF14495)	Thermosynechococcus elongatus (strain BP-1)	Cytochrome c-549,Cytochrome c550,Low-potential cytochrome c
17	KA, Q (Y, y)	Photosystem II reaction center protein Ycf12	polymer	46	5039.1	2	UniProt (Q8DJI1) Pfam (PF05969)	Thermosynechococcus elongatus (strain BP-1)
18	LA, R (X, x)	Photosystem II reaction center X protein	polymer	41	4322.2	2	UniProt (Q9F1R6) Pfam (PF06596)	Thermosynechococcus elongatus (strain BP-1)
19	MA, S (Z, z)	Photosystem II reaction center protein Z	polymer	62	6766.2	2	UniProt (Q8DHJ2) Pfam (PF01737)	Thermosynechococcus elongatus (strain BP-1)	PSII-Z
20	NA, T (R, r)	Photosystem II protein Y	polymer	41	4590.6	2	UniProt (Q8DKM3) Pfam (PF06298)	Thermosynechococcus elongatus (strain BP-1)
21	OA, ZD (A, a)	CA-MN4-O5 CLUSTER	non-polymer		339.8	2	Chemie (OEX)
22	AE, PA (a, A)	FE (II) ION	non-polymer		55.8	2	Chemie (FE2)
23	GB, HC, LD, MD, NF... (A, B, D, c, b...)	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	non-polymer		795.1	9	Chemie (SQD)
24	BE, CE, RA, SA (a, A)	CHLORIDE ION	non-polymer		35.5	4	Chemie (CL)
25	AF, AG, BF, BG, CB... (b, c, A, a, D...)	CHLOROPHYLL A	non-polymer		893.5	70	Chemie (CLA)
26	ED, GE, JG, VA (D, a, d, A)	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
27	AC, CG, DG, EH, HD... (B, c, y, D, b...)	BETA-CAROTENE	non-polymer		536.9	22	Chemie (BCR)
28	JE, KD, QG, YA (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)
29	AB, BC, BD, CC, CD... (A, B, C, c, D...)	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	16	Chemie (LMG)
30	AH, BB, BH, CH, DC... (m, A, t, B, C...)	UNKNOWN LIGAND	non-polymer		616.5	17	Chemie (UNL)
31	DB, EB, FB, JD, LE... (A, D, a, d, L...)	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	10	Chemie (LHG)
32	DE, HB (a, A)	BICARBONATE ION	non-polymer		61.0	2	Chemie (BCT)
33	AD, EG, FG, GG, QD... (C, c, H, h)	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	8	Chemie (DGD)
34	ND, SG (E, e)	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	2	Chemie (HEM)
35	DH, XD (v, V)	HEME C	non-polymer		618.5	2	Chemie (HEC)
36	AI, GH, HH, IH, JH... (v, A, B, C, D...)	water	water		18.0	124	Chemie (HOH)

Sequence modifications

I, i: 2 - 38 (UniProt: Q8DJZ6)

PDB	External Database	Details
Fme 1	-	expression tag

M, m: 2 - 36 (UniProt: Q8DHA7)

PDB	External Database	Details
Fme 1	-	expression tag

T, t: 2 - 32 (UniProt: Q8DIQ0)

PDB	External Database	Details
Fme 1	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	40
	Total formula weight	631653.0
Non-Polymers*	Number of molecules	174
	Total formula weight	129417.2
All*	Total formula weight	761070.2

*Water molecules are not included.