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)	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)	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)	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)	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)	Thermostichus vulcanus	PSII reaction center subunit V
6	F, X (F, f)	Cytochrome b559 subunit beta	polymer	44	4936.7	2	UniProt (P12239)	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)	Thermostichus vulcanus	PSII-H
8	H, Z (I, i)	Photosystem II reaction center protein I	polymer	38	4438.3	2	UniProt (P12240)	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)	Thermostichus vulcanus	PSII-J
10	BA, J (K, k)	Photosystem II reaction center protein K	polymer	37	4101.9	2	UniProt (P19054)	Thermostichus vulcanus	PSII-K
11	CA, K (L, l)	Photosystem II reaction center protein L	polymer	37	4299.0	2	UniProt (P12241)	Thermostichus vulcanus	PSII-L
12	DA, L (M, m)	Photosystem II reaction center protein M	polymer	36	4009.7	2	UniProt (P12312)	Thermostichus vulcanus	PSII-M
13	EA, M (O, o)	Photosystem II manganese-stabilizing polypeptide	polymer	244	26651.7	2	UniProt (D0VWR2)	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)	Thermostichus vulcanus	PSII-Tc
15	GA, O (U, u)	Photosystem II 12 kDa extrinsic protein	polymer	104	11656.0	2	UniProt (P56152)	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)	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)	Thermostichus vulcanus
18	JA, R (Y, y)	Photosystem II reaction center protein Ycf12	polymer	30	3228.0	2	UniProt (D0VWR3)	Thermostichus vulcanus
19	KA, MA (Z, z)	Photosystem II reaction center protein Z	polymer	62	6766.2	2	UniProt (D0VWR5)	Thermostichus vulcanus	PSII-Z
20	LA (R)	Photosystem II protein Y	polymer	34	3859.7	1	UniProt (P0DM37)	Thermostichus vulcanus
21	NA, SE (A, a)	FE (II) ION	non-polymer		55.8	2	Chemie (FE2) PubChem (27284)
22	OA, PA, TE, UE (A, a)	CHLORIDE ION	non-polymer		35.5	4	Chemie (CL) PubChem (312)
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) PubChem (573) PubChem (5315709) PubChem (5353436) PubChem (5356616) PubChem (5927371) PubChem (6477957) PubChem (9828626) PubChem (10256668) PubChem (12305639) PubChem (12305640) PubChem (12305642) PubChem (12305644) PubChem (12305647) PubChem (12305652) PubChem (21672398) PubChem (176490061) PubChem (177696266) PubChem (46783370) PubChem (46846294) PubChem (5280489) PubChem (92863345) PubChem (54603957) PubChem (54612003) PubChem (124919640) PubChem (146673260) PubChem (152743364) PubChem (160505766) PubChem (86765360) PubChem (91827292) PubChem (92863346) PubChem (92863347) PubChem (92863348) PubChem (100990628) PubChem (101525094) PubChem (101525095) PubChem (124919639) PubChem (129651951) PubChem (132274419) PubChem (145925599) PubChem (159562859) PubChem (172654026) PubChem (172878405) PubChem (173398668)
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) PubChem (5459390) PubChem (9810997) PubChem (9918745) PubChem (10219110) PubChem (10373133) PubChem (14463145) PubChem (25147486) PubChem (25235342) PubChem (42607399) PubChem (159321) PubChem (481096) PubChem (134765349) PubChem (102201395)
26	AJ, BC, BF, BI, EC... (v, B, a, d, C...)	GLYCEROL	non-polymer		92.1	21	Chemie (GOL) PubChem (753)
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) PubChem (20286) PubChem (5375177) PubChem (6323474) PubChem (6325820) PubChem (6433402) PubChem (23304240) PubChem (21881166)
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) PubChem (769)
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) PubChem (446440) PubChem (9547104) PubChem (11846227) PubChem (46936292) PubChem (65144) PubChem (13305396) PubChem (73416066) PubChem (138986743)
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) PubChem (561567) PubChem (656917) PubChem (10979306) PubChem (11335391) PubChem (11392262) PubChem (17754029) PubChem (22844385) PubChem (135074) PubChem (71317209) PubChem (95858610) PubChem (96361182) PubChem (96361183) PubChem (97041763) PubChem (101138253)
36	AD, BD, EH, FH, GH... (C, c, h, H)	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	8	Chemie (DGD) PubChem (448441) PubChem (24865462) PubChem (24865463) PubChem (46936671) PubChem (50904896) PubChem (447899) PubChem (4629344) PubChem (53480668) PubChem (15991538) PubChem (154573294) PubChem (171123158) PubChem (134746152) PubChem (140529801)
37	GD, HE, HI, KH, LH... (C, O, f, c, o...)	CALCIUM ION	non-polymer		40.1	7	Chemie (CA) PubChem (271)
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) PubChem (888)
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.