- PDB-6dhe: RT XFEL structure of the dark-stable state of Photosystem II (0F,... -
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Basic information
Entry
Database: PDB / ID: 6dhe
Title
RT XFEL structure of the dark-stable state of Photosystem II (0F, S1-rich) at 2.05 Angstrom resolution
Components
(Cytochrome b559 subunit ...) x 2
(Photosystem II ...) x 17
Cytochrome c-550
Keywords
PHOTOSYNTHESIS / PHOTOSYSTEMS / TRANSMEMBRANE / ROOM TEMPERATURE / ELECTRON TRANSPORT
Function / homology
Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II reaction centre protein Ycf12 / Photosystem II PsbL / Photosystem II PsbI / Photosystem II PsbK / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II CP43 reaction centre protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit ...Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II reaction centre protein Ycf12 / Photosystem II PsbL / Photosystem II PsbI / Photosystem II PsbK / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II CP43 reaction centre protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II PsbM / Cytochrome c-like domain / Photosystem II PsbY / Photosystem II PsbX / Photosystem II PsbU, oxygen evolving complex / Photosystem II PsbZ, reaction centre / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome c-550 precursor / Photosystem II CP47 reaction centre protein / Photosystem II PsbT superfamily / Photosystem II PsbX, type 1 subfamily / Cytochrome c-550 domain / Photosystem antenna protein-like superfamily / Photosystem II PsbZ superfamily / Photosystem II protein D1/D2 superfamily / Photosystem II reaction centre protein H superfamily / Cytochrome c-like domain superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Photosystem II PsbJ / Photosystem II PsbO, manganese-stabilising / Photosystem II PsbJ superfamily / Photosystem II PsbT / Cytochrome c family profile. / Cytochrome b559 subunits heme-binding site signature. / Photosynthetic reaction center proteins signature. / Cytochrome c-550 domain / Photosystem II reaction centre X protein (PsbX) / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II protein Y (PsbY) / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II 4 kDa reaction centre component / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / PsbL protein / PsbJ / YCF9 / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II PsbI superfamily / Photosystem II reaction centre protein H / Photosystem antenna protein-like / Photosynthetic reaction centre, L/M / Photosystem II PsbM superfamily / Photosystem II PsbK superfamily / Photosynthetic reaction centre protein / Photosystem II reaction centre T protein / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II protein / Photosystem II 10 kDa phosphoprotein / Photosystem II PsbL superfamily / oxygen evolving activity / photosystem II reaction center / photosystem II stabilization / photosystem II / photosystem II assembly / photosystem II oxygen evolving complex / photosystem II / cytochrome c-heme linkage / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / chlorophyll binding / thylakoid membrane / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / respiratory electron transport chain / phosphate ion binding / response to herbicide / photosynthesis / extrinsic component of membrane / protein-chromophore linkage / protein stabilization / manganese ion binding / oxidation-reduction process / electron transfer activity / iron ion binding / heme binding / integral component of membrane / metal ion binding / Cytochrome b559 subunit alpha / Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein K / Photosystem II protein Y / Photosystem II reaction center protein I / Photosystem II reaction center protein Ycf12 / Photosystem II reaction center protein H / Photosystem II CP47 reaction center protein
A: Photosystem II protein D1 1 B: Photosystem II CP47 reaction center protein C: Photosystem II CP43 reaction center protein D: Photosystem II D2 protein E: Cytochrome b559 subunit alpha F: Cytochrome b559 subunit beta H: Photosystem II reaction center protein H I: Photosystem II reaction center protein I J: Photosystem II reaction center protein J K: Photosystem II reaction center protein K L: Photosystem II reaction center protein L M: Photosystem II reaction center protein M O: Photosystem II manganese-stabilizing polypeptide T: Photosystem II reaction center protein T U: Photosystem II 12 kDa extrinsic protein V: Cytochrome c-550 Y: Photosystem II reaction center protein Ycf12 X: Photosystem II reaction center X protein Z: Photosystem II reaction center protein Z R: Photosystem II protein Y a: Photosystem II protein D1 1 b: Photosystem II CP47 reaction center protein c: Photosystem II CP43 reaction center protein d: Photosystem II D2 protein e: Cytochrome b559 subunit alpha f: Cytochrome b559 subunit beta h: Photosystem II reaction center protein H i: Photosystem II reaction center protein I j: Photosystem II reaction center protein J k: Photosystem II reaction center protein K l: Photosystem II reaction center protein L m: Photosystem II reaction center protein M o: Photosystem II manganese-stabilizing polypeptide t: Photosystem II reaction center protein T u: Photosystem II 12 kDa extrinsic protein v: Cytochrome c-550 y: Photosystem II reaction center protein Ycf12 x: Photosystem II reaction center X protein z: Photosystem II reaction center protein Z r: Photosystem II protein Y hetero molecules
Mass: 18.015 Da / Num. of mol.: 2021 / Formula: H2O / Water
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.4 / Density percent sol: 63.79 % / Description: Cube-like crystals
Crystal grow
Temp: 298 K / Method: batch mode / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000
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Data collection
Diffraction
ID
Mean temperature
Crystal ID
Serial crystal experiment
1
298
1
Y
3
298
1
Y
2
298
1
Y
Source
Source
Type
Synchrotron site
Beamline
Id
Wavelength
FREE ELECTRON LASER
SLAC LCLS BEAMLINE MFX
SLAC LCLS
MFX
1
1.305
FREE ELECTRON LASER
SLAC LCLS BEAMLINE MFX
SLAC LCLS
MFX
3
1.305
FREE ELECTRON LASER
SLAC LCLS BEAMLINE MFX
SLAC LCLS
MFX
2
1.305
Detector
Type
Id
Details
Detector
Collection date
RAYONIX MX170-HS
1
Compoundrefractivelenses
CCD
2016-07-14
RAYONIX MX170-HS
3
Compoundrefractivelenses
CCD
2017-07-13
RAYONIX MX170-HS
2
Compoundrefractivelenses
CCD
2016-10-20
Radiation
Id
Monochromator
Diffraction protocol
Monochromatic or laue m l
Scattering type
Wavelength ID
1
none
SINGLEWAVELENGTH
M
x-ray
1
3
none
SINGLEWAVELENGTH
M
x-ray
2
2
none
SINGLEWAVELENGTH
M
x-ray
3
Radiation wavelength
ID
Wavelength
Relative weight
1
1.305
1.0
2
1.305
1.0
3
1.305
1.0
Reflection
B iso Wilson estimate: 33.09 / D resolution high: 2.05 / D resolution low: 30.55 / Number obs: 497372 / CC half: .987 / NetI over sigmaI: 16.581 / Redundancy: 245.79 % / Percent possible obs: 99.96