5V2C

RE-REFINEMENT OF CRYSTAL STRUCTURE OF PHOTOSYSTEM II COMPLEX

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, a	Photosystem II protein D1	polymer	344	38235.6	2	UniProt (P51765) Pfam (PF00124) In PDB	Thermosynechococcus vulcanus	PSII D1 protein,Photosystem II Q(B) protein
2	B, b	Photosystem II CP47 reaction center protein	polymer	506	56141.7	2	UniProt (D0VWR1) Pfam (PF00421) In PDB	Thermosynechococcus vulcanus	PSII 47 kDa protein,Protein CP-47
3	C, c	Photosystem II CP43 reaction center protein	polymer	458	49940.0	2	UniProt (D0VWR7) Pfam (PF00421) In PDB	Thermosynechococcus vulcanus	PSII 43 kDa protein,Protein CP-43
4	D, d	Photosystem II D2 protein	polymer	342	38418.0	2	UniProt (D0VWR8) Pfam (PF00124) In PDB	Thermosynechococcus vulcanus	PSII D2 protein,Photosystem Q(A) protein
5	E, e	Cytochrome b559 subunit alpha	polymer	83	9449.6	2	UniProt (P12238) Pfam (PF00283) Pfam (PF00284) In PDB	Thermosynechococcus vulcanus	PSII reaction center subunit V
6	F, f	Cytochrome b559 subunit beta	polymer	44	4936.7	2	UniProt (P12239) Pfam (PF00283) In PDB	Thermosynechococcus vulcanus	PSII reaction center subunit VI
7	H, h	Photosystem II reaction center protein H	polymer	65	7227.6	2	UniProt (P19052) Pfam (PF00737) In PDB	Thermosynechococcus vulcanus	PSII-H
8	I, i	Photosystem II reaction center protein I	polymer	38	4438.3	2	UniProt (P12240) Pfam (PF02532) In PDB	Thermosynechococcus vulcanus	PSII-I,PSII 4.4 kDa protein
9	J, j	Photosystem II reaction center protein J	polymer	40	4103.8	2	UniProt (Q7DGD4) Pfam (PF01788) In PDB	Thermosynechococcus vulcanus	PSII-J
10	K, k	Photosystem II reaction center protein K	polymer	37	4101.9	2	UniProt (P19054) Pfam (PF02533) In PDB	Thermosynechococcus vulcanus	PSII-K
11	L, l	Photosystem II reaction center protein L	polymer	37	4299.0	2	UniProt (P12241) Pfam (PF02419) In PDB	Thermosynechococcus vulcanus	PSII-L
12	M, m	Photosystem II reaction center protein M	polymer	36	4009.7	2	UniProt (P12312) Pfam (PF05151) In PDB	Thermosynechococcus vulcanus	PSII-M
13	O, o	Photosystem II manganese-stabilizing polypeptide	polymer	245	26665.7	2	UniProt (D0VWR2) Pfam (PF01716) In PDB	Thermosynechococcus vulcanus	MSP
14	T, t	Photosystem II reaction center protein T	polymer	32	3906.7	2	UniProt (P12313) Pfam (PF01405) In PDB	Thermosynechococcus vulcanus	PSII-Tc
15	U, u	Photosystem II 12 kDa extrinsic protein	polymer	104	11656.0	2	UniProt (P56152) Pfam (PF06514) In PDB	Thermosynechococcus vulcanus	PS II complex 12 kDa extrinsic protein,PSII-U
16	V, v	Cytochrome c-550	polymer	137	15148.3	2	UniProt (P0A387) Pfam (PF14495) In PDB	Thermosynechococcus vulcanus	Cytochrome c550,Low-potential cytochrome c
17	Y, y	Photosystem II reaction center protein Ycf12	polymer	30	3228.0	2	UniProt (D0VWR3) Pfam (PF05969) In PDB	Thermosynechococcus vulcanus
18	X, x	Photosystem II reaction center protein X	polymer	41	4322.2	2	UniProt (D0VWR4) Pfam (PF06596) In PDB	Thermosynechococcus vulcanus
19	Z, z	Photosystem II reaction center protein Z	polymer	62	6766.2	2	UniProt (D0VWR5) Pfam (PF01737) In PDB	Thermosynechococcus vulcanus	PSII-Z
20	A, a	CA-MN4-O5 CLUSTER	non-polymer		339.8	2	Chemie (OEX)		PROTEIN CP-47
21	A, a	FE (II) ION	non-polymer		55.8	2	Chemie (FE2)
22	v, A, V, a	CHLORIDE ION	non-polymer		35.5	6	Chemie (CL)
23	m, A, a	BICARBONATE ION	non-polymer		61.0	3	Chemie (BCT)
24	B, C, b, d, D...	CHLOROPHYLL A	non-polymer		893.5	70	Chemie (CLA)
25	d, D, A, a	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
26	B, k, C, b, d...	BETA-CAROTENE	non-polymer		536.9	22	Chemie (BCR)
27	d, D, A, 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)
28	a, A, l, h, x...	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	non-polymer		795.1	11	Chemie (SQD)
29	a, c, B, b, C...	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	14	Chemie (LMG)
30	A, f, u, O, d...	GLYCEROL	non-polymer		92.1	60	Chemie (GOL)
31	A, u, I, c, B...	DODECYL-BETA-D-MALTOSIDE	non-polymer		510.6	18	Chemie (LMT)
32	E, A, l, a, d...	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	12	Chemie (LHG)
33	B, C, V, E, A...	TETRAETHYLENE GLYCOL	non-polymer		194.2	57	Chemie (PG4)
34	H, b, B, f, C...	TRIETHYLENE GLYCOL	non-polymer		150.2	65	Chemie (PGE)
35	j, C, A, I, b...	HEXAETHYLENE GLYCOL	non-polymer		282.3	17	Chemie (P6G)
36	H, C, V, O, I...	1,2-ETHANEDIOL	non-polymer		62.1	22	Chemie (EDO)
37	h, c, B, o, b...	CALCIUM ION	non-polymer		40.1	6	Chemie (CA)
38	O, h, a, c, B...	heptyl 1-thio-beta-D-glucopyranoside	non-polymer		294.4	24	Chemie (HTG)
39	j, V, B, x, L...	PENTAETHYLENE GLYCOL	non-polymer		238.3	7	Chemie (1PE)
40	c, C, h, d, D...	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	10	Chemie (DGD)
41	E, e	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	2	Chemie (HEM)
42	J, F, j, f	MAGNESIUM ION	non-polymer		24.3	4	Chemie (MG)
43	v, V	HEME C	non-polymer		618.5	2	Chemie (HEC)
44	V	NONAETHYLENE GLYCOL	non-polymer		414.5	1	Chemie (2PE)
45	i	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL	non-polymer		370.4	1	Chemie (PE8)
46		water	water		18.0	3787	Chemie (HOH)

Sequence modifications

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

PDB	External Database	Details
Pro 279	Arg 279	conflict

B, b: 2 - 505 (UniProt: D0VWR1)

PDB	External Database	Details
Ser 506	-	expression tag
Asp 507	-	expression tag

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

PDB	External Database	Details
Glu 16	-	expression tag
Ala 17	-	expression tag
Ala 18	-	expression tag
Asn 19	-	expression tag
Ser 20	-	expression tag
Ile 21	-	expression tag
Phe 22	-	expression tag

J, j: 1 - 40 (UniProt: Q7DGD4)

PDB	External Database	Details
Glu 2	Met 2	conflict

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

O, o: 4 - 246 (UniProt: D0VWR2)

PDB	External Database	Details
Ala 2	-	expression tag
Ala 3	-	expression tag

X, x: 2 - 41 (UniProt: D0VWR4)

PDB	External Database	Details
Met 1	-	initiating methionine

Contents of the asymmetric unit

Polymers	Number of chains	38
	Total formula weight	593990.2
Non-Polymers*	Number of molecules	446
	Total formula weight	173999.6
All*	Total formula weight	767989.8

*Water molecules are not included.