5B66 image
Deposition Date 2016-05-25
Release Date 2017-02-01
Last Version Date 2024-10-23
Entry Detail
PDB ID:
5B66
Title:
Crystal structure analysis of Photosystem II complex
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.85 Å
R-Value Free:
0.20
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein D1
Gene (Uniprot):psbA
Chain IDs:A, T (auth: a)
Chain Length:344
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP47 reaction center protein
Gene (Uniprot):psbB
Chain IDs:B, U (auth: b)
Chain Length:505
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 reaction center protein
Gene (Uniprot):psbC
Chain IDs:C, V (auth: c)
Chain Length:455
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD
Chain IDs:D, W (auth: d)
Chain Length:342
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
Chain IDs:E, X (auth: e)
Chain Length:83
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
Chain IDs:F, Y (auth: f)
Chain Length:44
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein H
Gene (Uniprot):psbH
Chain IDs:G (auth: H), Z (auth: h)
Chain Length:65
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein I
Gene (Uniprot):psbI
Chain IDs:H (auth: I), AA (auth: i)
Chain Length:38
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein J
Gene (Uniprot):psbJ
Chain IDs:I (auth: J), BA (auth: j)
Chain Length:40
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein K
Gene (Uniprot):psbK
Chain IDs:J (auth: K), CA (auth: k)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein L
Gene (Uniprot):psbL
Chain IDs:K (auth: L), DA (auth: l)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein M
Gene (Uniprot):psbM
Chain IDs:L (auth: M), EA (auth: m)
Chain Length:36
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II manganese-stabilizing polypeptide
Gene (Uniprot):psbO
Chain IDs:M (auth: O), FA (auth: o)
Chain Length:244
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
Chain IDs:N (auth: T), GA (auth: t)
Chain Length:32
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II 12 kDa extrinsic protein
Gene (Uniprot):psbU
Chain IDs:O (auth: U), HA (auth: u)
Chain Length:104
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c-550
Gene (Uniprot):psbV
Chain IDs:P (auth: V), IA (auth: v)
Chain Length:137
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein X
Gene (Uniprot):psbX
Chain IDs:R (auth: X), KA (auth: x)
Chain Length:40
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Ycf12
Gene (Uniprot):psb30
Chain IDs:Q (auth: Y), JA (auth: y)
Chain Length:30
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
Chain IDs:S (auth: Z), LA (auth: z)
Chain Length:62
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME H MET modified residue
Primary Citation
Two Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II
J. Am. Chem. Soc. 139 1718 1721 (2017)
PMID: 28102667 DOI: 10.1021/jacs.6b09666

Abstact

The oxygen-evolving complex (OEC) forms the heart of photosystem II (PSII) in photosynthesis. The crystal structure of PSII from Thermosynechococcus vulcanus has been reported at a resolution of 1.9 Å and at an averaged X-ray dose of 0.43 MGy. The OEC structure is suggested to be partially reduced to Mn(II) by EXAFS and DFT computational studies. Recently, the "radiation-damage-free" structures have been published at 1.95 Å resolution using XFEL, but reports continued to appear that the OEC is reduced to the S0-state of the Kok cycle. To elucidate much more precise structure of the OEC, in this study two structures were determined at extremely low X-ray doses of 0.03 and 0.12 MGy using conventional synchrotron radiation source. The results indicated that the X-ray reduction effects on the OEC were very small in the low dose region below 0.12 MGy, that is, a threshold existed for the OEC structural changes caused by X-ray exposure. The OEC structures of the two identical monomers in the crystal were clearly different under the threshold of the radiation dose, although the surrounding polypeptide frameworks of PSII were the same. The assumption that the OECs in the crystal were in the dark-stable S1-state of the Kok cycle should be re-evaluated.

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