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- PDB-7z8d: Structure of Photosynthetic Reaction Center From Rhodobacter Spha... -

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Basic information

Entry
Database: PDB / ID: 7z8d
TitleStructure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV by fixed-target serial synchrotron crystallography (room temperature, 26keV)
Components(Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS / Photosynthetic reaction center / bacteriochlorophyll / Rhodobacter sphaeroides / serial crystallography / mesophase crystallization / lipid sponge phase / lipid cubic phase / spheroidene / ubiquinone
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / : / photosynthesis, light reaction / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / 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 / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily ...Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / 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 / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / DODECANE / : / PENTADECANE / Chem-NKP / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-10 ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / DODECANE / : / PENTADECANE / Chem-NKP / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-10 / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain
Similarity search - Component
Biological speciesCereibacter sphaeroides 2.4.1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsGabdulkhakov, A.G. / Selikhanov, G.K. / Guenther, S. / Petrova, T. / Meents, A. / Fufina, T.Y. / Vasilieva, L.G.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-02-40008_mega Russian Federation
CitationJournal: To Be Published
Title: Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV by fixed-target serial synchrotron crystallography (room temperature, 26keV)
Authors: Gabdulkhakov, A.G. / Selikhanov, G.K. / Guenther, S. / Meents, A. / Fufina, T.Y. / Vasilieva, L.G.
History
DepositionMar 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
H: Reaction center protein H chain
L: Reaction center protein L chain
M: Reaction center protein M chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,55625
Polymers91,5313
Non-polymers10,02522
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37550 Å2
ΔGint-211 kcal/mol
Surface area29170 Å2
Unit cell
Length a, b, c (Å)102.500, 102.500, 237.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

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

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


Mass: 26284.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides 2.4.1 (bacteria)
Gene: puhA / Production host: Cereibacter sphaeroides 2.4.1 (bacteria) / Strain (production host): RV / References: UniProt: P0C0Y7
#2: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 31360.416 Da / Num. of mol.: 1 / Mutation: S178T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides 2.4.1 (bacteria)
Gene: pufL / Production host: Cereibacter sphaeroides 2.4.1 (bacteria) / References: UniProt: P0C0Y8
#3: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 33885.922 Da / Num. of mol.: 1 / Mutation: S8T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides 2.4.1 (bacteria)
Gene: pufM / Production host: Cereibacter sphaeroides 2.4.1 (bacteria) / Strain (production host): RV / References: UniProt: P0C0Y9

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Non-polymers , 13 types, 201 molecules

#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26
#8: Chemical ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H32
#9: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#10: Chemical ChemComp-NKP / (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate / 18:1 LPA / oleoyl lysophosphatidic acid


Mass: 436.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H41O7P
#11: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#15: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.41 Å3/Da / Density % sol: 63.89 %
Crystal growTemperature: 289 K / Method: small tubes
Details: 1-mono-oleyl-rac-glycerol (MO), 1,2,3-heptanetriol, Jeffamine M600, N,N-dimethyldodecylamine-N-oxide (LDAO)

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.4769 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.4769 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 70474 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 38.14 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.18 / Net I/σ(I): 10.06
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 1.38 / Num. unique obs: 5099 / CC1/2: 0.54 / Rrim(I) all: 1.9 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: Roadruner / Sample holding: silicon chip

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6z1j

6z1j


Resolution: 2.14→47.05 Å / SU ML: 0.2604 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7241
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2133 3542 5.03 %
Rwork0.1792 66932 -
obs0.1809 70474 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.4 Å2
Refinement stepCycle: LAST / Resolution: 2.14→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6487 0 712 179 7378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00737762
X-RAY DIFFRACTIONf_angle_d0.953410620
X-RAY DIFFRACTIONf_chiral_restr0.04981060
X-RAY DIFFRACTIONf_plane_restr0.00811307
X-RAY DIFFRACTIONf_dihedral_angle_d19.09512752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.170.35891490.34622571X-RAY DIFFRACTION99.13
2.17-2.20.29021440.29572623X-RAY DIFFRACTION99.78
2.2-2.230.29611490.26742655X-RAY DIFFRACTION100
2.23-2.270.29041230.26052652X-RAY DIFFRACTION100
2.27-2.310.33991300.25932617X-RAY DIFFRACTION100
2.31-2.340.2831340.24152654X-RAY DIFFRACTION99.96
2.34-2.390.28361410.23212669X-RAY DIFFRACTION100
2.39-2.430.28921390.22312611X-RAY DIFFRACTION100
2.43-2.480.28311240.22492665X-RAY DIFFRACTION99.96
2.48-2.540.2431420.22382656X-RAY DIFFRACTION99.96
2.54-2.60.25341460.21112648X-RAY DIFFRACTION99.96
2.6-2.660.25271470.20052656X-RAY DIFFRACTION100
2.66-2.730.2451180.18372671X-RAY DIFFRACTION99.93
2.73-2.810.20131370.16832655X-RAY DIFFRACTION100
2.81-2.90.18071470.16642679X-RAY DIFFRACTION100
2.9-3.010.21541320.15642673X-RAY DIFFRACTION100
3.01-3.130.21611640.16412648X-RAY DIFFRACTION100
3.13-3.270.21511410.15992684X-RAY DIFFRACTION100
3.27-3.440.19241580.1452687X-RAY DIFFRACTION100
3.44-3.660.1441560.14472689X-RAY DIFFRACTION100
3.66-3.940.17961530.14082698X-RAY DIFFRACTION100
3.94-4.340.19171480.14922708X-RAY DIFFRACTION100
4.34-4.960.18751330.15432767X-RAY DIFFRACTION99.97
4.97-6.250.21521440.18622787X-RAY DIFFRACTION100
6.25-47.050.19581430.1842909X-RAY DIFFRACTION97.48

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