8IRD

XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 20-nanosecond delay

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, S (A, a)	Photosystem II protein D1	polymer	344	38235.6	2	UniProt (P51765) Pfam (PF00124)	Thermostichus vulcanus	PSII D1 protein,Photosystem II Q(B) protein
2	B, T (B, b)	Photosystem II CP47 reaction center protein	polymer	505	56068.7	2	UniProt (D0VWR1) Pfam (PF00421)	Thermostichus vulcanus	PSII 47 kDa protein,Protein CP-47
3	C, U (C, c)	Photosystem II CP43 reaction center protein	polymer	455	49668.8	2	UniProt (D0VWR7) Pfam (PF00421)	Thermostichus vulcanus	PSII 43 kDa protein,Protein CP-43
4	D, V (D, d)	Photosystem II D2 protein	polymer	342	38404.9	2	UniProt (D0VWR8) Pfam (PF00124)	Thermostichus vulcanus	PSII D2 protein,Photosystem Q(A) protein
5	E, W (E, e)	Cytochrome b559 subunit alpha	polymer	84	9580.8	2	UniProt (P12238) Pfam (PF00283) Pfam (PF00284)	Thermostichus vulcanus	PSII reaction center subunit V
6	F, X (F, f)	Cytochrome b559 subunit beta	polymer	44	4936.7	2	UniProt (P12239) Pfam (PF00283)	Thermostichus vulcanus	PSII reaction center subunit VI
7	G, Y (H, h)	Photosystem II reaction center protein H	polymer	65	7227.6	2	UniProt (P19052) Pfam (PF00737)	Thermostichus vulcanus	PSII-H
8	H, Z (I, i)	Photosystem II reaction center protein I	polymer	38	4438.3	2	UniProt (P12240) Pfam (PF02532)	Thermostichus vulcanus	PSII-I,PSII 4.4 kDa protein
9	AA, I (J, j)	Photosystem II reaction center protein J	polymer	39	3974.7	2	UniProt (Q7DGD4) Pfam (PF01788)	Thermostichus vulcanus	PSII-J
10	BA, J (K, k)	Photosystem II reaction center protein K	polymer	37	4101.9	2	UniProt (P19054) Pfam (PF02533)	Thermostichus vulcanus	PSII-K
11	CA, K (L, l)	Photosystem II reaction center protein L	polymer	37	4299.0	2	UniProt (P12241) Pfam (PF02419)	Thermostichus vulcanus	PSII-L
12	DA, L (M, m)	Photosystem II reaction center protein M	polymer	36	4009.7	2	UniProt (P12312) Pfam (PF05151)	Thermostichus vulcanus	PSII-M
13	EA, M (O, o)	Photosystem II manganese-stabilizing polypeptide	polymer	244	26651.7	2	UniProt (D0VWR2) Pfam (PF01716)	Thermostichus vulcanus	MSP,Extrinsic protein O of oxygen-evolving complex
14	FA, N (T, t)	Photosystem II reaction center protein T	polymer	32	3906.7	2	UniProt (P12313) Pfam (PF01405)	Thermostichus vulcanus	PSII-Tc
15	GA, O (U, u)	Photosystem II 12 kDa extrinsic protein	polymer	104	11656.0	2	UniProt (P56152) Pfam (PF06514)	Thermostichus vulcanus	PS II complex 12 kDa extrinsic protein,PSII-U
16	HA, P (V, v)	Cytochrome c-550	polymer	137	15148.3	2	UniProt (P0A387) Pfam (PF14495)	Thermostichus vulcanus	Cytochrome c550,Low-potential cytochrome c,Extrinsic protein V of oxygen-evolving complex
17	IA, Q (X, x)	Photosystem II reaction center protein X	polymer	40	4191.0	2	UniProt (D0VWR4) Pfam (PF06596)	Thermostichus vulcanus
18	JA, R (Y, y)	Photosystem II reaction center protein Ycf12	polymer	30	3228.0	2	UniProt (D0VWR3) Pfam (PF05969)	Thermostichus vulcanus
19	KA, MA (Z, z)	Photosystem II reaction center protein Z	polymer	62	6766.2	2	UniProt (D0VWR5) Pfam (PF01737)	Thermostichus vulcanus	PSII-Z
20	LA (R)	Photosystem II protein Y	polymer	34	3859.7	1	UniProt (P0DM37) Pfam (PF06298)	Thermostichus vulcanus
21	NA, SE (A, a)	FE (II) ION	non-polymer		55.8	2	Chemie (FE2)
22	OA, PA, TE, UE (A, a)	CHLORIDE ION	non-polymer		35.5	4	Chemie (CL)
23	AG, AH, BH, GB, HB... (b, c, B, D, C...)	CHLOROPHYLL A	non-polymer		893.5	70	Chemie (CLA)
24	BG, BJ, CG, CH, DG... (b, y, c, K, h...)	BETA-CAROTENE	non-polymer		536.9	22	Chemie (BCR)
25	AF, CF, EG, GI, NI... (a, b, f, l, X...)	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	non-polymer		795.1	8	Chemie (SQD)
26	AJ, BC, BF, BI, EC... (v, B, a, d, C...)	GLYCEROL	non-polymer		92.1	21	Chemie (GOL)
27	DF, YA (a, A)	CA-MN4-O5 CLUSTER	non-polymer		339.8	2	Chemie (OEX)
28	EF, MD, UH, ZA (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, AE, BE, DC, DE... (A, I, J, B, K...)	UNKNOWN LIGAND	non-polymer		61.0	18	Chemie (UNL)
30	BB, PH (A, d)	BICARBONATE ION	non-polymer		61.0	2	Chemie (BCT)
31	CB, GF, HD, XE (A, a, D)	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
32	DB, EI, FB, FC, FG... (A, e, B, b, M...)	DODECYL-BETA-D-MALTOSIDE	non-polymer		510.6	14	Chemie (LMT)
33	CI, EB, FE, KF, ND... (d, A, L, a, D...)	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	10	Chemie (LHG)
34	AI, CD, CJ, DD, DJ... (d, C, Z, z, c...)	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	12	Chemie (LMG)
35	AC, CC, ED, GG, HG... (B, C, b, c, V...)	heptyl 1-thio-beta-D-glucopyranoside	non-polymer		294.4	11	Chemie (HTG)
36	AD, BD, EH, FH, GH... (C, c, h, H)	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	8	Chemie (DGD)
37	GD, HE, HI, KH, LH... (C, O, f, c, o...)	CALCIUM ION	non-polymer		40.1	7	Chemie (CA)
38	FI, WD (f, F)	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	2	Chemie (HEM)
39	CE, LI (J, j)	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG)
40	ME, ZI (V, v)	HEME C	non-polymer		618.5	2	Chemie (HEC)
41	AK, BK, CK, DK, EJ... (f, h, i, j, A...)	water	water		18.0	1823	Chemie (HOH)

Sequence modifications

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

PDB	External Database	Details
Pro 279	Arg 279	conflict

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

PDB	External Database	Details
Asn 19	-	expression tag
Ser 20	-	expression tag
Ile 21	-	expression tag
Phe 22	-	expression tag

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

PDB	External Database	Details
Leu 33	Phe 24	conflict
Trp 39	Val 30	conflict

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

PDB	External Database	Details
Leu 8	Phe 8	conflict

Contents of the asymmetric unit

Polymers	Number of chains	39
	Total formula weight	596849.1
Non-Polymers*	Number of molecules	225
	Total formula weight	128741.7
All*	Total formula weight	725590.8

*Water molecules are not included.