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Entry
Database: PDB / ID: 7m75
TitleRoom Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two phylloquinones in Photosystem I
Components(Photosystem I ...) x 12
KeywordsPHOTOSYNTHESIS / Membrane complex / Electron transport
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI / Photosystem I 4.8K protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKeable, S.M. / Simon, P.S. / Kolsch, A. / Kern, J. / Yachandra, V.K. / Zouni, A. / Yano, J.
Funding support United States, Germany, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126289 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110501 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM055302 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117126 United States
Department of Energy (DOE, United States) United States
German Research Foundation (DFG)SFB1078 Germany
German Research Foundation (DFG)EXEC 2008/1 - 390540038 Germany
CitationJournal: Sci Rep / Year: 2021
Title: Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I.
Authors: Keable, S.M. / Kolsch, A. / Simon, P.S. / Dasgupta, M. / Chatterjee, R. / Subramanian, S.K. / Hussein, R. / Ibrahim, M. / Kim, I.S. / Bogacz, I. / Makita, H. / Pham, C.C. / Fuller, F.D. / ...Authors: Keable, S.M. / Kolsch, A. / Simon, P.S. / Dasgupta, M. / Chatterjee, R. / Subramanian, S.K. / Hussein, R. / Ibrahim, M. / Kim, I.S. / Bogacz, I. / Makita, H. / Pham, C.C. / Fuller, F.D. / Gul, S. / Paley, D. / Lassalle, L. / Sutherlin, K.D. / Bhowmick, A. / Moriarty, N.W. / Young, I.D. / Blaschke, J.P. / de Lichtenberg, C. / Chernev, P. / Cheah, M.H. / Park, S. / Park, G. / Kim, J. / Lee, S.J. / Park, J. / Tono, K. / Owada, S. / Hunter, M.S. / Batyuk, A. / Oggenfuss, R. / Sander, M. / Zerdane, S. / Ozerov, D. / Nass, K. / Lemke, H. / Mankowsky, R. / Brewster, A.S. / Messinger, J. / Sauter, N.K. / Yachandra, V.K. / Yano, J. / Zouni, A. / Kern, J.
History
DepositionMar 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,413147
Polymers257,29012
Non-polymers107,123135
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60710 Å2
ΔGint-429 kcal/mol
Surface area110460 Å2
2
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules

A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules

A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,036,010426
Polymers721,61230
Non-polymers314,398396
Water48627
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area181640 Å2
ΔGint-1353 kcal/mol
Surface area305700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)285.429, 285.429, 166.543
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

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Photosystem I ... , 12 types, 12 molecules ABCDEFIJKLMX

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / / PsaA


Mass: 83267.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A405, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PsaB


Mass: 82992.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A407, photosystem I
#3: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8678.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A415, photosystem I
#4: Protein Photosystem I reaction center subunit II / / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15258.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A420
#5: Protein Photosystem I reaction center subunit IV / / Photosystem I 8.1 kDa protein / p30 protein


Mass: 8268.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A423
#6: Protein Photosystem I reaction center subunit III / / PSI-F


Mass: 17716.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A401
#7: Protein/peptide Photosystem I reaction center subunit VIII /


Mass: 4297.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A427
#8: Protein/peptide Photosystem I reaction center subunit IX /


Mass: 4770.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A429
#9: Protein Photosystem I reaction center subunit PsaK / / Light-harvesting 8.0 kDa polypeptide / Photosystem I subunit X


Mass: 8483.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A425
#10: Protein Photosystem I reaction center subunit XI / / PSI subunit V / PSI-L


Mass: 16156.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DGB4
#11: Protein/peptide Photosystem I reaction center subunit XII / / PSI-M


Mass: 3426.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A403
#12: Protein/peptide Photosystem I 4.8K protein /


Mass: 3973.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DKP6

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Sugars , 2 types, 2 molecules

#21: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#22: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C51H96O15

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Non-polymers , 9 types, 252 molecules

#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 95 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#15: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#17: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10
#18: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#19: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#20: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#23: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 7.61 Å3/Da / Density % sol: 83.84 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 5 mM MES, pH 6.0, 12 mM sodium sulfate, 0.2% beta-dodecyl maltoside

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.305 Å
DetectorType: RAYONIX MX170-HS / Detector: CCD / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.305 Å / Relative weight: 1
ReflectionResolution: 2.75→56.71 Å / Num. obs: 199647 / % possible obs: 99.98 % / Redundancy: 506.39 % / Biso Wilson estimate: 68.4 Å2 / CC1/2: 0.998 / Net I/σ(I): 3.6
Reflection shellResolution: 2.75→2.79 Å / Num. unique obs: 9949 / CC1/2: 0.135

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Processing

Software
NameVersionClassification
cctbx.xfeldata reduction
PHENIX1.19.1_4122refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JB0

1jb0


Resolution: 2.75→56.71 Å / SU ML: 0.5395 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.4932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2792 1903 1 %
Rwork0.264 187689 -
obs0.2641 189592 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.3 Å2
Refinement stepCycle: LAST / Resolution: 2.75→56.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17524 0 6869 119 24512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005825747
X-RAY DIFFRACTIONf_angle_d0.991336455
X-RAY DIFFRACTIONf_chiral_restr0.05073144
X-RAY DIFFRACTIONf_plane_restr0.00784568
X-RAY DIFFRACTIONf_dihedral_angle_d18.52854402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.366750.39788341X-RAY DIFFRACTION59.29
2.82-2.890.43281150.396111821X-RAY DIFFRACTION84.1
2.89-2.980.37951370.372313253X-RAY DIFFRACTION93.91
2.98-3.080.38861430.357513593X-RAY DIFFRACTION97.05
3.08-3.190.36221390.347314025X-RAY DIFFRACTION99.4
3.19-3.310.36521450.349814046X-RAY DIFFRACTION99.82
3.31-3.460.34151440.323114058X-RAY DIFFRACTION99.75
3.46-3.650.32581440.309414065X-RAY DIFFRACTION99.77
3.65-3.880.31291430.309214063X-RAY DIFFRACTION99.65
3.88-4.170.28791430.269414056X-RAY DIFFRACTION99.64
4.18-4.590.24591460.244113981X-RAY DIFFRACTION98.97
4.59-5.260.22451430.221813991X-RAY DIFFRACTION99.02
5.26-6.620.23041380.234214131X-RAY DIFFRACTION99.4
6.62-56.710.22741480.188714265X-RAY DIFFRACTION99.4

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