9PHW

Structure of the D1-Val185Asn mutated photosystem II complex with slow O-O bond formation reveals changes in the Cl1 water channel

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, V (A, a)	Photosystem II protein D1 2	polymer	344	38295.5	2	UniProt (P16033) Pfam (PF00124)	Synechocystis sp. PCC 6803	PSII D1 protein 2,Photosystem II Q(B) protein 2
2	B, W (B, b)	Photosystem II CP47 reaction center protein	polymer	513	56783.2	2	UniProt (P05429) Pfam (PF00421)	Synechocystis sp. PCC 6803
3	C, X (C, c)	Photosystem II CP43 reaction center protein	polymer	460	50344.7	2	UniProt (P09193) Pfam (PF00421)	Synechocystis sp. PCC 6803
4	D, Y (D, d)	Photosystem II D2 protein	polymer	352	39519.2	2	UniProt (P09192) Pfam (PF00124)	Synechocystis sp. PCC 6803
5	E, Z (E, e)	Cytochrome b559 subunit alpha	polymer	81	9454.6	2	UniProt (P09190) Pfam (PF00283) Pfam (PF00284)	Synechocystis sp. PCC 6803
6	AA, F (F, f)	Cytochrome b559 subunit beta	polymer	44	4935.8	2	UniProt (P09191) Pfam (PF00283)	Synechocystis sp. PCC 6803
7	BA, G (H, h)	Photosystem II reaction center protein H	polymer	64	7120.4	2	UniProt (P14835) Pfam (PF00737)	Synechocystis sp. PCC 6803
8	CA, H (I, i)	Photosystem II reaction center protein I	polymer	38	4338.1	2	UniProt (Q54697) Pfam (PF02532)	Synechocystis sp. PCC 6803
9	DA, I (J, j)	Photosystem II reaction center protein J	polymer	35	3470.1	2	UniProt (P73070) Pfam (PF01788)	Synechocystis sp. PCC 6803	PSII-J
10	EA, J (K, k)	Photosystem II reaction center protein K	polymer	45	5114.1	2	UniProt (P15819) Pfam (PF02533)	Synechocystis sp. PCC 6803
11	FA, K (L, l)	Photosystem II reaction center protein L	polymer	39	4476.1	2	UniProt (Q55354) Pfam (PF02419)	Synechocystis sp. PCC 6803
12	GA, L (M, m)	Photosystem II reaction center protein M	polymer	35	3910.6	2	UniProt (P72701) Pfam (PF05151)	Synechocystis sp. PCC 6803
13	HA, M (O, o)	Photosystem II manganese-stabilizing polypeptide	polymer	274	29939.6	2	UniProt (P10549) Pfam (PF01716)	Synechocystis sp. PCC 6803
14	IA, N (Q, q)	Sll1638 protein	polymer	149	16494.9	2	UniProt (P73048) Pfam (PF05757)	Synechocystis sp. PCC 6803
15	JA, O (R, r)	Photosystem II protein Y	polymer	39	4205.0	2	UniProt (P73676) Pfam (PF06298)	Synechocystis sp. PCC 6803
16	KA, P (T, t)	Photosystem II reaction center protein T	polymer	31	3571.3	2	UniProt (P74787) Pfam (PF01405)	Synechocystis sp. PCC 6803
17	LA, Q (U, u)	Photosystem II 12 kDa extrinsic protein	polymer	131	14256.2	2	UniProt (Q55332) Pfam (PF06514)	Synechocystis sp. PCC 6803
18	MA, R (V, v)	Cytochrome c-550	polymer	160	17901.0	2	UniProt (Q55013) Pfam (PF14495)	Synechocystis sp. PCC 6803
19	NA, S (X, x)	Photosystem II reaction center X protein	polymer	39	4189.0	2	UniProt (P72575) Pfam (PF06596)	Synechocystis sp. PCC 6803
20	OA, T (Y, y)	Photosystem II reaction center protein Ycf12	polymer	39	4144.0	2	UniProt (Q55438) Pfam (PF05969)	Synechocystis sp. PCC 6803
21	PA, U (Z, z)	Photosystem II reaction center protein Z	polymer	62	6736.2	2	UniProt (P73528) Pfam (PF01737)	Synechocystis sp. PCC 6803
22	CF, QA (a, A)	CA-MN4-O5 CLUSTER	non-polymer		339.8	2	Chemie (OEX)
23	DF, RA (a, A)	FE (II) ION	non-polymer		55.8	2	Chemie (FE2) PubChem (27284)
24	EF, FF, SA, TA (a, A)	CHLORIDE ION	non-polymer		35.5	4	Chemie (CL) PubChem (312)
25	AG, AH, BG, BH, CG... (b, c, B, a, C...)	CHLOROPHYLL A	non-polymer		893.5	70	Chemie (CLA)
26	IF, LD, WA, XH (a, D, A, d)	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
27	AF, GC, IH, JG, JI... (Z, B, c, b, f...)	BETA-CAROTENE	non-polymer		536.9	18	Chemie (BCR) PubChem (573) PubChem (21672398) PubChem (176490061) PubChem (177696266) PubChem (46783370) PubChem (46846294) PubChem (54603957) PubChem (54612003) PubChem (5315709) PubChem (5353436) PubChem (5356616) PubChem (5927371) PubChem (86765360) PubChem (6477957) PubChem (9828626) PubChem (91827292) PubChem (10256668) PubChem (92863346) PubChem (92863347) PubChem (92863348) PubChem (12305639) PubChem (12305640) PubChem (12305642) PubChem (12305644) PubChem (12305647) PubChem (12305652) PubChem (5280489) PubChem (92863345) PubChem (100990628) PubChem (101525094) PubChem (101525095) PubChem (124919640) PubChem (124919639) PubChem (129651951) PubChem (132274419) PubChem (146673260) PubChem (152743364) PubChem (160505766) PubChem (145925599) PubChem (159562859) PubChem (172654026) PubChem (172878405) PubChem (173398668)
28	AD, CI, DB, JE, LF... (C, d, A, J, a...)	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	14	Chemie (LMG)
29	AB, AI, MF, OD (A, d, a, 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) PubChem (20286) PubChem (23304240) PubChem (21881166) PubChem (5375177) PubChem (6323474) PubChem (6325820) PubChem (6433402)
30	BB, CB, CE, IC, KE... (A, H, C, K, f...)	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	non-polymer		795.1	14	Chemie (SQD) PubChem (25147486) PubChem (25235342) PubChem (42607399) PubChem (5459390) PubChem (159321) PubChem (9810997) PubChem (9918745) PubChem (481096) PubChem (10219110) PubChem (10373133) PubChem (14463145) PubChem (102201395) PubChem (134765349)
31	AC, AE, AJ, BC, BD... (B, F, t, C, d...)	DODECYL-BETA-D-MALTOSIDE	non-polymer		510.6	62	Chemie (LMT)
32	FB, RF (A, a)	BICARBONATE ION	non-polymer		61.0	2	Chemie (BCT) PubChem (769)
33	BF, BI, GI, HC, HD... (Z, d, e, B, D...)	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	14	Chemie (LHG) PubChem (446440) PubChem (46936292) PubChem (73416066) PubChem (65144) PubChem (9547104) PubChem (11846227) PubChem (13305396) PubChem (138986743)
34	DE, GD, JH, KH, OI... (H, C, c, h)	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	8	Chemie (DGD) PubChem (24865462) PubChem (24865463) PubChem (448441) PubChem (50904896) PubChem (53480668) PubChem (46936671) PubChem (447899) PubChem (4629344) PubChem (15991538) PubChem (134746152) PubChem (154573294) PubChem (140529801) PubChem (171123158)
35	CJ, II, UE, XD (v, e, V, E)	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	4	Chemie (HEM)
36	BE, MI (H, h)	(3R)-beta,beta-caroten-3-ol	non-polymer		552.9	2	Chemie (RRX) PubChem (20056910) PubChem (92111) PubChem (177443103) PubChem (182237) PubChem (44554791) PubChem (5316150) PubChem (6384256) PubChem (91496173) PubChem (5281235) PubChem (101088204) PubChem (124934401) PubChem (102330248) PubChem (102330249) PubChem (102330250) PubChem (124934402) PubChem (124934403) PubChem (124934404) PubChem (152743353) PubChem (163007083) PubChem (163007084) PubChem (168433814) PubChem (169423484)
37	BJ, DJ, LE, TE, VE... (u, v, K, U, V...)	CALCIUM ION	non-polymer		40.1	6	Chemie (CA) PubChem (271)
38	AK, BK, CK, DK, EK... (V, X, a, b, c...)	water	water		18.0	1016	Chemie (HOH)

Sequence modifications

A, a: 1 - 344 (UniProt: P16033)

PDB	External Database	Details
Asn 185	Val 185	engineered mutation

B, b: 1 - 507 (UniProt: P05429)

PDB	External Database	Details
His 508	-	expression tag
His 509	-	expression tag
His 510	-	expression tag
His 511	-	expression tag
His 512	-	expression tag
His 513	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	42
	Total formula weight	658399.6
Non-Polymers*	Number of molecules	230
	Total formula weight	155082.8
All*	Total formula weight	813482.4

*Water molecules are not included.