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- PDB-8c88: Double mutant G(M19)C/T(L214)C structure of Photosynthetic Reacti... -

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Basic information

Entry
Database: PDB / ID: 8c88
TitleDouble mutant G(M19)C/T(L214)C structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV
Components(Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS / Photosynthetic reaction center / bacteriochlorophyll / Rhodobacter sphaeroides / spheroidene / ubiquinone / disulfide bond
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 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, 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.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / 1,4-DIETHYLENE DIOXIDE / : / Chem-NKP / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-10 / Unknown ligand ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / 1,4-DIETHYLENE DIOXIDE / : / Chem-NKP / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-10 / Unknown ligand / 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: 2.75 Å
AuthorsGabdulkhakov, A. / Selikhanov, G. / Fufina, T. / Vasilieva, L. / Atamas, A. / Yukhimchuk, D.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-02-40008 Russian Federation
CitationJournal: Membranes (Basel) / Year: 2023
Title: Stabilization of Cereibacter sphaeroides Photosynthetic Reaction Center by the Introduction of Disulfide Bonds.
Authors: Selikhanov, G. / Atamas, A. / Yukhimchuk, D. / Fufina, T. / Vasilieva, L. / Gabdulkhakov, A.
History
DepositionJan 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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
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)101,71934
Polymers91,7103
Non-polymers10,00931
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40550 Å2
ΔGint-178 kcal/mol
Surface area29580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.910, 100.910, 237.020
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)
Strain: RV / Gene: puhA / Production host: Cereibacter sphaeroides 2.4.1 (bacteria) / References: UniProt: P0C0Y7
#2: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 31362.455 Da / Num. of mol.: 1 / Mutation: S178T, T214C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides 2.4.1 (bacteria)
Strain: RV / 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: 34063.207 Da / Num. of mol.: 1 / Mutation: S8T, G19C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides 2.4.1 (bacteria)
Strain: RV / Gene: pufM / Production host: Cereibacter sphaeroides 2.4.1 (bacteria) / References: UniProt: P0C0Y9

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Non-polymers , 13 types, 54 molecules

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


Mass: 229.402 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#6: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 7 / Source method: obtained synthetically
#7: 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 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


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


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#11: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#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-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 32119 / % possible obs: 98.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 70.28 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.11 / Net I/σ(I): 7.92
Reflection shellResolution: 2.75→2.82 Å / Mean I/σ(I) obs: 1.06 / Num. unique obs: 2369 / CC1/2: 0.4 / Rrim(I) all: 1.24

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→46.42 Å / SU ML: 0.4686 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.2593
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2706 1282 3.99 %
Rwork0.1991 30809 -
obs0.202 32091 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.93 Å2
Refinement stepCycle: LAST / Resolution: 2.75→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6499 0 781 23 7303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00957572
X-RAY DIFFRACTIONf_angle_d1.234410317
X-RAY DIFFRACTIONf_chiral_restr0.0571029
X-RAY DIFFRACTIONf_plane_restr0.00981255
X-RAY DIFFRACTIONf_dihedral_angle_d17.6722705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.860.42241410.34633403X-RAY DIFFRACTION99.83
2.86-2.990.36021410.2923394X-RAY DIFFRACTION99.63
2.99-3.150.29711440.25053433X-RAY DIFFRACTION99.5
3.15-3.340.34451420.23373421X-RAY DIFFRACTION99.66
3.35-3.60.27841430.20513444X-RAY DIFFRACTION99.72
3.6-3.970.25191410.17613394X-RAY DIFFRACTION97.92
3.97-4.540.27561430.16313420X-RAY DIFFRACTION97.88
4.54-5.720.22721330.17473232X-RAY DIFFRACTION90.9
5.72-46.420.24171540.19113668X-RAY DIFFRACTION97.65

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