4RVY: Serial Time resolved crystallography of Photosystem II using a femtosecond X-ray laser. The S state after two flashes (S3)

PDB ID: 4RVYDownload
MMDB ID: 133839
PDB Deposition Date: 2014/11/29
Updated in MMDB: 2022/11
Experimental Method:
x-ray diffraction
Resolution: 5.5  Å
Source Organism:
Similar Structures:
Biological Unit for 4RVY: 38-meric; determined by author
Molecular Components in 4RVY
Label Count Molecule
Proteins (38 molecules)
2
Photosystem II Protein D1 1
(Gene symbol: psbA1)
Molecule annotation
2
Photosystem II Cp47 Reaction Center Protein
(Gene symbol: psbB)
Molecule annotation
2
Photosystem II Cp43 Reaction Center Protein
(Gene symbol: psbC)
Molecule annotation
2
Photosystem II D2 Protein
(Gene symbol: psbD1)
Molecule annotation
2
Cytochrome B559 Subunit Alpha
(Gene symbol: psbE)
Molecule annotation
2
Cytochrome B559 Subunit Beta
(Gene symbol: psbF)
Molecule annotation
2
Photosystem II Reaction Center Protein H
(Gene symbol: psbH)
Molecule annotation
2
Photosystem II Reaction Center Protein I
(Gene symbol: psbI)
Molecule annotation
2
Photosystem II Reaction Center Protein J
(Gene symbol: psbJ)
Molecule annotation
2
Photosystem II Reaction Center Protein K
(Gene symbol: psbK)
Molecule annotation
2
Photosystem II Reaction Center Protein L
(Gene symbol: psbL)
Molecule annotation
2
Photosystem II Reaction Center Protein M
(Gene symbol: psbM)
Molecule annotation
2
Photosystem II Manganese-stabilizing Polypeptide
(Gene symbol: psbO)
Molecule annotation
2
Photosystem II Reaction Center Protein T
(Gene symbol: psbT)
Molecule annotation
2
Photosystem II 12 KDA Extrinsic Protein
(Gene symbol: psbU)
Molecule annotation
2
Cytochrome C-550
(Gene symbol: psbV)
Molecule annotation
2
Photosystem II Reaction Center X Protein
(Gene symbol: psbX)
Molecule annotation
2
Photosystem II Reaction Center Protein Ycf12
(Gene symbol: ycf12)
Molecule annotation
2
Photosystem II Reaction Center Protein Z
(Gene symbol: psbZ)
Molecule annotation
Chemicals and Non-standard biopolymers (166 molecules)
1
2
CA-MN4-O5 CLUSTERCA-MN4-O5 CLUSTER
2
2
FE (II) IONFE (II) ION
3
70
CHLOROPHYLL ACHLOROPHYLL A
4
4
PHEOPHYTIN APHEOPHYTIN A
5
22
BETA-CAROTENEBETA-CAROTENE
6
10
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
7
6
CHLORIDE IONCHLORIDE ION
8
2
BICARBONATE IONBICARBONATE ION
9
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
10
12
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
11
6
CALCIUM IONCALCIUM ION
12
10
DIGALACTOSYL DIACYL GLYCEROL (DGDG)DIGALACTOSYL DIACYL GLYCEROL (DGDG)
13
10
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
14
4
PROTOPORPHYRIN IX CONTAINING FEPROTOPORPHYRIN IX CONTAINING FE
15
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