5GTH

Native XFEL structure of photosystem II (dark dataset)

Summary for 5GTH

Related5GTI 4UB6
DescriptorPhotosystem II protein D1, Photosystem II CP47 reaction center protein, Photosystem II CP43 reaction center protein, ... (40 entities in total)
Functional Keywordsphotosystem ii, photosynthesis, psii, membrane protein
Biological sourceThermosynechococcus vulcanus
Cellular locationCellular thylakoid membrane ; Multi-pass membrane protein  D0VWR1 D0VWR8 D0VWR5
Cellular thylakoid membrane ; Single-pass membrane protein  P12238 P12239 P19052 P12240 Q7DGD4 P12241 P12313 D0VWR4 D0VWR3 P0DM37
Cellular thylakoid membrane ; Peripheral membrane protein ; Lumenal side  D0VWR2 P56152 P0A387
Total number of polymer chains39
Total molecular weight734577.08
Authors
Suga, M.,Shen, J.R. (deposition date: 2016-08-20, release date: 2017-03-15)
Primary citation
Suga, M.,Akita, F.,Sugahara, M.,Kubo, M.,Nakajima, Y.,Nakane, T.,Yamashita, K.,Umena, Y.,Nakabayashi, M.,Yamane, T.,Nakano, T.,Suzuki, M.,Masuda, T.,Inoue, S.,Kimura, T.,Nomura, T.,Yonekura, S.,Yu, L.J.,Sakamoto, T.,Motomura, T.,Chen, J.H.,Kato, Y.,Noguchi, T.,Tono, K.,Joti, Y.,Kameshima, T.,Hatsui, T.,Nango, E.,Tanaka, R.,Naitow, H.,Matsuura, Y.,Yamashita, A.,Yamamoto, M.,Nureki, O.,Yabashi, M.,Ishikawa, T.,Iwata, S.,Shen, J.R.
Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.
Nature, 543:131-135, 2017
PubMed: 28219079 (PDB entries with the same primary citation)
DOI: 10.1038/nature21400
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.5 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.18750.1%1.6%10.8%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5gth
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Molmil generated image of 5gth
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Molmil generated image of 5gth
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More Biological unit images

Molmil generated image of 5gth
no rotation
Molmil generated image of 5gth
rotated about x axis by 90°
Molmil generated image of 5gth
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5gth.pdb1.gz [1.1 MB])
Coordinate files for Biological unit (5gth.pdb2.gz [1.07 MB])