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- PDB-7q7q: LIPIDIC CUBIC PHASE SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE ... -

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Basic information

Entry
Database: PDB / ID: 7q7q
TitleLIPIDIC CUBIC PHASE SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE OF A PHOTOSYNTHETIC REACTION CENTRE
Components
  • (Reaction center protein ...Photosynthetic reaction centre) x 3
  • Photosynthetic reaction center cytochrome c subunit
KeywordsMEMBRANE PROTEIN / CRYSTALLOGRAPHY STRUCTURE PHOTOSYNTHETIC REACTION CENTRE
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / HEPTANE-1,2,3-TRIOL / MENAQUINONE-9 / 15-cis-1,2-dihydroneurosporene / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / UBIQUINONE-2 ...BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / HEPTANE-1,2,3-TRIOL / MENAQUINONE-9 / 15-cis-1,2-dihydroneurosporene / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / UBIQUINONE-2 / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBaath, P. / Banacore, A. / Neutze, R.
Funding supportEuropean Union, Sweden, 2items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH)789030European Union
European Research Council (ERC)2015-00560 Sweden
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre.
Authors: Bath, P. / Banacore, A. / Borjesson, P. / Bosman, R. / Wickstrand, C. / Safari, C. / Dods, R. / Ghosh, S. / Dahl, P. / Ortolani, G. / Bjorg Ulfarsdottir, T. / Hammarin, G. / Garcia Bonete, M. ...Authors: Bath, P. / Banacore, A. / Borjesson, P. / Bosman, R. / Wickstrand, C. / Safari, C. / Dods, R. / Ghosh, S. / Dahl, P. / Ortolani, G. / Bjorg Ulfarsdottir, T. / Hammarin, G. / Garcia Bonete, M.J. / Vallejos, A. / Ostojic, L. / Edlund, P. / Linse, J.B. / Andersson, R. / Nango, E. / Owada, S. / Tanaka, R. / Tono, K. / Joti, Y. / Nureki, O. / Luo, F. / James, D. / Nass, K. / Johnson, P.J.M. / Knopp, G. / Ozerov, D. / Cirelli, C. / Milne, C. / Iwata, S. / Branden, G. / Neutze, R.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_validate_chiral
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
CCC: Photosynthetic reaction center cytochrome c subunit
HHH: Reaction center protein H chain
LLL: Reaction center protein L chain
MMM: Reaction center protein M chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,92542
Polymers132,4104
Non-polymers14,51538
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Purity confirmed with spectrophotometer at A830 nm.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56320 Å2
ΔGint-417 kcal/mol
Surface area41090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.660, 125.130, 182.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11MMM-564-

HOH

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Components

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Protein , 1 types, 1 molecules CCC

#1: Protein Photosynthetic reaction center cytochrome c subunit / Cytochrome c558/c559


Mass: 37450.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastochloris viridis (bacteria) / Gene: pufC, cytC, BVIRIDIS_00500 / Production host: Blastochloris viridis (bacteria) / References: UniProt: P07173

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Reaction center protein ... , 3 types, 3 molecules HHHLLLMMM

#2: Protein Reaction center protein H chain / Photosynthetic reaction centre / Photosynthetic reaction center H subunit


Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06008
#3: Protein Reaction center protein L chain / Photosynthetic reaction centre / Photosynthetic reaction center L subunit


Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06009
#4: Protein Reaction center protein M chain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit


Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06010

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Non-polymers , 13 types, 305 molecules

#5: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Chemical ChemComp-DGA / DIACYL GLYCEROL / Diglyceride


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#7: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#8: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#9: Chemical
ChemComp-BCB / BACTERIOCHLOROPHYLL B / Bacteriochlorophyll


Mass: 909.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O6
#10: Chemical ChemComp-BPB / BACTERIOPHEOPHYTIN B / Pheophytin


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6
#11: Chemical
ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H16O3
#12: Chemical ChemComp-UQ2 / UBIQUINONE-2


Mass: 318.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H26O4
#13: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#14: Chemical ChemComp-MQ9 / MENAQUINONE-9 / Vitamin K2


Mass: 785.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H80O2
#15: Chemical ChemComp-NS5 / 15-cis-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60
#16: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#17: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.65 Å3/Da / Density % sol: 66.28 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: This LCP crystallization was performed in wells with 200uL precipitant and 20uL LCP+protein.

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Room Temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.102 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.102 Å / Relative weight: 1
ReflectionResolution: 2.25→23.702 Å / Num. obs: 92545 / % possible obs: 100 % / Redundancy: 11.888 % / CC1/2: 0.995 / Net I/σ(I): 9.6
Reflection shellResolution: 2.25→2.27 Å / Num. unique obs: 92545 / CC1/2: 0.54
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionFlow rate: 0.047 µL/min / Injector diameter: 75 µm / Injector temperature: 293 K
Serial crystallography data reductionCrystal hits: 260392 / Frames indexed: 160275

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFEL0.9.0data reduction
CrystFEL0.9.0data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NJ4

5nj4


Resolution: 2.25→23.702 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.515 / SU ML: 0.126 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2028 4602 4.974 %
Rwork0.1678 87913 -
all0.169 --
obs-92515 99.856 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.613 Å20 Å20 Å2
2--1.99 Å2-0 Å2
3----2.602 Å2
Refinement stepCycle: LAST / Resolution: 2.25→23.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9263 0 1022 267 10552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310703
X-RAY DIFFRACTIONr_bond_other_d0.0020.01710106
X-RAY DIFFRACTIONr_angle_refined_deg2.131.76214640
X-RAY DIFFRACTIONr_angle_other_deg1.2031.69323128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58151177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06220.4500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84151407
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg16.304151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7531566
X-RAY DIFFRACTIONr_chiral_restr0.0740.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211746
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022538
X-RAY DIFFRACTIONr_nbd_refined0.1950.21948
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.29096
X-RAY DIFFRACTIONr_nbtor_refined0.1680.24911
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24652
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2344
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0860.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0980.26
X-RAY DIFFRACTIONr_nbd_other0.1570.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0620.22
X-RAY DIFFRACTIONr_mcbond_it2.8734.7394705
X-RAY DIFFRACTIONr_mcbond_other2.8714.7384704
X-RAY DIFFRACTIONr_mcangle_it4.3727.1055877
X-RAY DIFFRACTIONr_mcangle_other4.3727.1055878
X-RAY DIFFRACTIONr_scbond_it3.5155.3285998
X-RAY DIFFRACTIONr_scbond_other3.5145.3295999
X-RAY DIFFRACTIONr_scangle_it5.5947.7548761
X-RAY DIFFRACTIONr_scangle_other5.5947.7558762
X-RAY DIFFRACTIONr_lrange_it7.35853.19412043
X-RAY DIFFRACTIONr_lrange_other7.35853.20112044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.3080.3073630.3066412X-RAY DIFFRACTION100
2.308-2.3720.2933140.2836265X-RAY DIFFRACTION100
2.372-2.440.3333410.2726111X-RAY DIFFRACTION100
2.44-2.5160.2772960.2485946X-RAY DIFFRACTION100
2.516-2.5980.2583430.2265697X-RAY DIFFRACTION100
2.598-2.6890.2452840.2075571X-RAY DIFFRACTION100
2.689-2.7910.2242730.1855391X-RAY DIFFRACTION100
2.791-2.9050.1722670.1585199X-RAY DIFFRACTION100
2.905-3.0340.1952510.154983X-RAY DIFFRACTION100
3.034-3.1820.2052360.1554761X-RAY DIFFRACTION100
3.182-3.3540.1722210.1484567X-RAY DIFFRACTION100
3.354-3.5570.182120.1394308X-RAY DIFFRACTION100
3.557-3.8030.1592010.1314080X-RAY DIFFRACTION100
3.803-4.1070.1581960.1283789X-RAY DIFFRACTION100
4.107-4.4990.1481950.1263484X-RAY DIFFRACTION100
4.499-5.030.1651720.133190X-RAY DIFFRACTION100
5.03-5.8070.1821510.1472810X-RAY DIFFRACTION100
5.807-7.110.1941340.1442414X-RAY DIFFRACTION100
7.11-10.0480.138930.1261911X-RAY DIFFRACTION100
10.048-23.7020.705590.504991X-RAY DIFFRACTION88.7574

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