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- PDB-8c5x: Double mutant A(L37)C/S(L99)C structure of Photosynthetic Reactio... -

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Basic information

Entry
Database: PDB / ID: 8c5x
TitleDouble mutant A(L37)C/S(L99)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 / CARDIOLIPIN / 1,4-DIETHYLENE DIOXIDE / : / HEPTANE-1,2,3-TRIOL / : / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-10 ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / 1,4-DIETHYLENE DIOXIDE / : / HEPTANE-1,2,3-TRIOL / : / 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: 2.6 Å
AuthorsGabdulkhakov, A. / Selikhanov, G. / Fufina, T. / Vasilieva, L. / Atamas, A. / Uhimchuk, 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 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)103,73446
Polymers91,7103
Non-polymers12,02443
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47060 Å2
ΔGint-168 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.850, 139.850, 186.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: 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: 31408.545 Da / Num. of mol.: 1 / Mutation: A37C, S99C
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: 34017.117 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: pufM / Production host: Cereibacter sphaeroides 2.4.1 (bacteria) / References: UniProt: P0C0Y9

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Non-polymers , 14 types, 149 molecules

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


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 10 / Source method: obtained synthetically
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


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


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#13: Chemical ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#14: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#15: 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
#16: Chemical ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2 / Feature type: SUBJECT OF INVESTIGATION
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 5.74 Å3/Da / Density % sol: 78.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 3.5% 1,2,3 -heptanetriol, 2% dioxane, 0.1% LDAO, 1M potassium phosphate

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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: Feb 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 65303 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 52.72 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.13
Reflection shellResolution: 2.6→2.67 Å / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 4784 / CC1/2: 0.57 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.89 Å / SU ML: 0.2728 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6743
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2074 3351 5.13 %
Rwork0.1856 61950 -
obs0.1868 65301 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.3 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6472 0 923 106 7501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917685
X-RAY DIFFRACTIONf_angle_d1.122210441
X-RAY DIFFRACTIONf_chiral_restr0.05491028
X-RAY DIFFRACTIONf_plane_restr0.00891260
X-RAY DIFFRACTIONf_dihedral_angle_d17.47022768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.30341530.25952567X-RAY DIFFRACTION100
2.64-2.680.28821150.24672555X-RAY DIFFRACTION100
2.68-2.720.25281440.24882517X-RAY DIFFRACTION99.92
2.72-2.760.25771400.22652567X-RAY DIFFRACTION100
2.76-2.810.25071430.22332559X-RAY DIFFRACTION99.96
2.81-2.860.2251210.20632562X-RAY DIFFRACTION99.93
2.86-2.920.28191130.21522619X-RAY DIFFRACTION100
2.92-2.980.27871310.19812540X-RAY DIFFRACTION100
2.98-3.040.21741560.20762537X-RAY DIFFRACTION100
3.04-3.110.30861220.20072616X-RAY DIFFRACTION100
3.11-3.190.21121210.19732565X-RAY DIFFRACTION100
3.19-3.280.18871070.18752580X-RAY DIFFRACTION100
3.28-3.370.21371220.18312597X-RAY DIFFRACTION100
3.37-3.480.18561210.17122579X-RAY DIFFRACTION99.96
3.48-3.60.19941410.17952566X-RAY DIFFRACTION100
3.6-3.750.21631560.17332539X-RAY DIFFRACTION99.89
3.75-3.920.22061160.16712597X-RAY DIFFRACTION99.63
3.92-4.120.21641520.15922572X-RAY DIFFRACTION99.93
4.12-4.380.1671560.1622579X-RAY DIFFRACTION99.96
4.38-4.720.16791620.1472564X-RAY DIFFRACTION100
4.72-5.190.17531460.16712623X-RAY DIFFRACTION100
5.19-5.940.17911650.1852576X-RAY DIFFRACTION100
5.94-7.460.17911670.19442651X-RAY DIFFRACTION99.96
7.46-29.890.22841810.20952723X-RAY DIFFRACTION99.86

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