5H2F: Crystal structure of the PsbM-deletion mutant of photosystem II

PDB ID: 5H2FDownload
MMDB ID: 148496
PDB Deposition Date: 2016/10/15
Updated in MMDB: 2023/11
Experimental Method:
x-ray diffraction
Resolution: 2.2  Å
Source Organism:
Similar Structures:
Biological Unit for 5H2F: octadecameric; determined by author
Molecular Components in 5H2F
Label Count Molecule
Proteins (18 molecules)
1
Photosystem II Protein D1 1
(Gene symbol: psbA1)
Molecule annotation
1
Photosystem II Cp47 Reaction Center Protein
(Gene symbol: psbB)
Molecule annotation
1
Photosystem II Cp43 Reaction Center Protein
(Gene symbol: psbC)
Molecule annotation
1
Photosystem II D2 Protein
(Gene symbol: psbD1)
Molecule annotation
1
Cytochrome B559 Subunit Alpha
(Gene symbol: psbE)
Molecule annotation
1
Cytochrome B559 Subunit Beta
(Gene symbol: psbF)
Molecule annotation
1
Photosystem II Reaction Center Protein H
(Gene symbol: psbH)
Molecule annotation
1
Photosystem II Reaction Center Protein I
(Gene symbol: psbI)
Molecule annotation
1
Photosystem II Reaction Center Protein J
(Gene symbol: psbJ)
Molecule annotation
1
Photosystem II Reaction Center Protein K
(Gene symbol: psbK)
Molecule annotation
1
Photosystem II Reaction Center Protein L
(Gene symbol: psbL)
Molecule annotation
1
Photosystem II Manganese-stabilizing Polypeptide
(Gene symbol: psbO)
Molecule annotation
1
Photosystem II Reaction Center Protein T
(Gene symbol: psbT)
Molecule annotation
1
Photosystem II 12 KDA Extrinsic Protein
(Gene symbol: psbU)
Molecule annotation
1
Cytochrome C-550
(Gene symbol: psbV)
Molecule annotation
1
Photosystem II Reaction Center Protein Ycf12
(Gene symbol: ycf12)
Molecule annotation
1
Photosystem II Reaction Center X Protein
(Gene symbol: psbX)
Molecule annotation
1
Photosystem II Reaction Center Protein Z
(Gene symbol: psbZ)
Molecule annotation
Chemicals and Non-standard biopolymers (182 molecules)
1
1
CA-MN4-O5 CLUSTERCA-MN4-O5 CLUSTER
2
1
FE (II) IONFE (II) ION
3
2
CHLORIDE IONCHLORIDE ION
4
35
CHLOROPHYLL ACHLOROPHYLL A
5
2
PHEOPHYTIN APHEOPHYTIN A
6
11
BETA-CAROTENEBETA-CAROTENE
7
6
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
8
2
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
9
6
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
10
6
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
11
8
DODECYL-BETA-D-MALTOSIDEDODECYL-BETA-D-MALTOSIDE
12
66
DIMETHYL SULFOXIDEDIMETHYL SULFOXIDE
13
1
BICARBONATE IONBICARBONATE ION
14
2
CALCIUM IONCALCIUM ION
15
11
heptyl 1-thio-beta-D-glucopyranosideheptyl 1-thio-beta-D-glucopyranoside
16
12
UNKNOWN LIGANDUNKNOWN LIGAND
17
5
DIGALACTOSYL DIACYL GLYCEROL (DGDG)DIGALACTOSYL DIACYL GLYCEROL (DGDG)
18
1
PROTOPORPHYRIN IX CONTAINING FEPROTOPORPHYRIN IX CONTAINING FE
19
1
(3R)-beta,beta-caroten-3-ol(3R)-beta,beta-caroten-3-ol
20
2
MAGNESIUM IONMAGNESIUM ION
21
1
HEME CHEME C
* 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