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Entry
Database: PDB / ID: 7m76
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 / oxidoreductase activity ...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 / oxidoreductase activity / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / 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 PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / 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 PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / 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 / Up-down Bundle / Mainly Alpha
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: 3 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61210 Å2
ΔGint-434 kcal/mol
Surface area109470 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
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

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
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

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
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)1,068,434438
Polymers747,06433
Non-polymers321,369405
Water27015
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 area186350 Å2
ΔGint-1399 kcal/mol
Surface area311080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)284.269, 284.269, 165.746
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: saccharide / 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, 153 molecules

#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


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


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


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#16: Chemical...
ChemComp-BCR / BETA-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


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#19: Chemical ChemComp-SF4 / 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


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 7.36 Å3/Da / Density % sol: 83.3 %
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: PAL-XFEL / Beamline: NCI / Wavelength: 1.277 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.277 Å / Relative weight: 1
ReflectionResolution: 3→25.23 Å / Num. obs: 147785 / % possible obs: 100 % / Redundancy: 32 % / Biso Wilson estimate: 74.47 Å2 / CC1/2: 0.904 / Net I/σ(I): 1.3
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 7378 / CC1/2: 0.31

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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: 3→25.23 Å / SU ML: 0.6008 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.0033
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2783 1944 1.32 %
Rwork0.268 145366 -
obs0.2681 147310 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.26 Å2
Refinement stepCycle: LAST / Resolution: 3→25.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17524 0 6869 20 24413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006125747
X-RAY DIFFRACTIONf_angle_d1.076236455
X-RAY DIFFRACTIONf_chiral_restr0.05333144
X-RAY DIFFRACTIONf_plane_restr0.00874568
X-RAY DIFFRACTIONf_dihedral_angle_d18.82144402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.38751110.37268302X-RAY DIFFRACTION77.93
3.07-3.160.35761360.37049619X-RAY DIFFRACTION90.53
3.16-3.250.35781370.362910251X-RAY DIFFRACTION96.37
3.25-3.360.38181410.366110513X-RAY DIFFRACTION98.33
3.36-3.470.35911420.358510546X-RAY DIFFRACTION99.24
3.48-3.610.39221370.354210591X-RAY DIFFRACTION99.1
3.61-3.780.35731420.341110672X-RAY DIFFRACTION99.74
3.78-3.980.33281390.314410613X-RAY DIFFRACTION99.71
3.98-4.220.29021440.290810671X-RAY DIFFRACTION99.75
4.22-4.550.27471440.265110658X-RAY DIFFRACTION99.87
4.55-50.27031410.261210691X-RAY DIFFRACTION99.76
5-5.720.30481400.247910706X-RAY DIFFRACTION99.85
5.72-7.180.22591460.23210743X-RAY DIFFRACTION99.83
7.18-25.230.17861440.171310790X-RAY DIFFRACTION99.18

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