6JLK: XFEL structure of cyanobacterial photosystem II (1F state, dataset1)

PDB ID: 6JLKDownload
MMDB ID: 180445
PDB Deposition Date: 2019/3/6
Updated in MMDB: 2024/12
Experimental Method:
x-ray diffraction
Resolution: 2.15  Å
Source Organism:
Similar Structures:
Biological Unit for 6JLK: 39-meric; determined by author
Molecular Components in 6JLK
Label Count Molecule
Proteins (39 molecules)
2
Photosystem II Protein D1
Molecule annotation
2
Photosystem II Cp47 Reaction Center Protein
Molecule annotation
2
Photosystem II Cp43 Reaction Center Protein
Molecule annotation
2
Photosystem II D2 Protein
Molecule annotation
2
Cytochrome B559 Subunit Alpha
Molecule annotation
2
Cytochrome B559 Subunit Beta
Molecule annotation
2
Photosystem II Reaction Center Protein H
Molecule annotation
2
Photosystem II Reaction Center Protein I
Molecule annotation
2
Photosystem II Reaction Center Protein J
Molecule annotation
2
Photosystem II Reaction Center Protein K
Molecule annotation
2
Photosystem II Reaction Center Protein L
Molecule annotation
2
Photosystem II Reaction Center Protein M
Molecule annotation
2
Photosystem II Manganese-stabilizing Polypeptide
Molecule annotation
2
Photosystem II Reaction Center Protein T
Molecule annotation
2
Photosystem II 12 KDA Extrinsic Protein
Molecule annotation
2
Cytochrome C-550
Molecule annotation
2
Photosystem II Reaction Center Protein Ycf12
Molecule annotation
2
Photosystem II Reaction Center Protein X
Molecule annotation
2
Photosystem II Reaction Center Protein Z
Molecule annotation
1
Photosystem II Protein Y
Molecule annotation
Chemicals and Non-standard biopolymers (251 molecules)
1
2
FE (II) IONFE (II) ION
2
6
CHLORIDE IONCHLORIDE ION
3
2
BICARBONATE IONBICARBONATE ION
4
70
CHLOROPHYLL ACHLOROPHYLL A
5
4
PHEOPHYTIN APHEOPHYTIN A
6
22
BETA-CAROTENEBETA-CAROTENE
7
8
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
8
35
GLYCEROLGLYCEROL
9
14
DODECYL-BETA-D-MALTOSIDEDODECYL-BETA-D-MALTOSIDE
10
2
CA-MN4-O5 CLUSTERCA-MN4-O5 CLUSTER
11
4
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-BENZOQUINONE2,3-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
12
18
UNKNOWN LIGANDUNKNOWN LIGAND
13
12
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
14
9
CALCIUM IONCALCIUM ION
15
17
heptyl 1-thio-beta-D-glucopyranosideheptyl 1-thio-beta-D-glucopyranoside
16
10
DIGALACTOSYL DIACYL GLYCEROL (DGDG)DIGALACTOSYL DIACYL GLYCEROL (DGDG)
17
10
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
18
4
PROTOPORPHYRIN IX CONTAINING FEPROTOPORPHYRIN IX CONTAINING FE
19
2
MAGNESIUM IONMAGNESIUM ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303