4FBY image
Deposition Date 2012-05-23
Release Date 2012-06-20
Last Version Date 2024-11-20
Entry Detail
PDB ID:
4FBY
Keywords:
Title:
fs X-ray diffraction of Photosystem II
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
6.56 Å
R-Value Free:
0.38
R-Value Work:
0.36
R-Value Observed:
0.36
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Photosystem Q(B) protein 1
Gene (Uniprot):psbA1
Chain IDs:A, U (auth: G)
Chain Length:38
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II core light harvesting protein
Gene (Uniprot):psbB
Chain IDs:B, V (auth: N)
Chain Length:39
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 protein
Gene (Uniprot):psbC
Chain IDs:C, W (auth: P)
Chain Length:461
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD1, psbD2
Chain IDs:D, X (auth: Q)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
Chain IDs:E, Y (auth: R)
Chain Length:83
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
Chain IDs:F, Z (auth: S)
Chain Length:246
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein H
Gene (Uniprot):psbH
Chain IDs:G (auth: H), AA (auth: W)
Chain Length:104
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein I
Gene (Uniprot):psbI
Chain IDs:H (auth: I), BA (auth: a)
Chain Length:38
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein J
Gene (Uniprot):psbJ
Chain IDs:I (auth: J), CA (auth: b)
Chain Length:39
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein K
Gene (Uniprot):psbK
Chain IDs:J (auth: K), DA (auth: c)
Chain Length:461
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein L
Gene (Uniprot):psbL
Chain IDs:K (auth: L), EA (auth: d)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein M
Gene (Uniprot):psbM
Chain IDs:L (auth: M), FA (auth: e)
Chain Length:83
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II manganese-stabilizing polypeptide
Gene (Uniprot):psbO
Chain IDs:M (auth: O), GA (auth: f)
Chain Length:246
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
Chain IDs:N (auth: T), HA (auth: g)
Chain Length:32
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II 12 kDa extrinsic protein
Gene (Uniprot):psbU
Chain IDs:O (auth: U), IA (auth: h)
Chain Length:104
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c-550
Gene (Uniprot):psbV
Chain IDs:P (auth: V), JA (auth: i)
Chain Length:38
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein X
Gene (Uniprot):psbX
Chain IDs:R (auth: X), LA (auth: j)
Chain Length:40
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Y
Chain IDs:S (auth: Y), MA (auth: k)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
Chain IDs:T (auth: Z), NA (auth: l)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein ycf12
Gene (Uniprot):psb30
Chain IDs:Q (auth: y), KA (auth: m)
Chain Length:46
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Primary Citation

Abstact

Most of the dioxygen on earth is generated by the oxidation of water by photosystem II (PS II) using light from the sun. This light-driven, four-photon reaction is catalyzed by the Mn(4)CaO(5) cluster located at the lumenal side of PS II. Various X-ray studies have been carried out at cryogenic temperatures to understand the intermediate steps involved in the water oxidation mechanism. However, the necessity for collecting data at room temperature, especially for studying the transient steps during the O-O bond formation, requires the development of new methodologies. In this paper we report room temperature X-ray diffraction data of PS II microcrystals obtained using ultrashort (< 50 fs) 9 keV X-ray pulses from a hard X-ray free electron laser, namely the Linac Coherent Light Source. The results presented here demonstrate that the "probe before destroy" approach using an X-ray free electron laser works even for the highly-sensitive Mn(4)CaO(5) cluster in PS II at room temperature. We show that these data are comparable to those obtained in synchrotron radiation studies as seen by the similarities in the overall structure of the helices, the protein subunits and the location of the various cofactors. This work is, therefore, an important step toward future studies for resolving the structure of the Mn(4)CaO(5) cluster without any damage at room temperature, and of the reaction intermediates of PS II during O-O bond formation.

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