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- PDB-8c7c: Double mutant V(M84)C/A(L278)C structure of Photosynthetic Reacti... -

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Basic information

Entry
Database: PDB / ID: 8c7c
TitleDouble mutant V(M84)C/A(L278)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 / : / HEPTANE-1,2,3-TRIOL / 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 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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)102,56331
Polymers92,6173
Non-polymers9,94628
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42070 Å2
ΔGint-167 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)253.130, 75.980, 65.850
Angle α, β, γ (deg.)90.000, 95.580, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-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: 27189.297 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) / References: UniProt: P0C0Y7
#2: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 31406.506 Da / Num. of mol.: 1 / Mutation: G278C
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: 34021.129 Da / Num. of mol.: 1 / Mutation: V84C
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 , 11 types, 49 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-UNL / UNKNOWN LIGAND


Num. of mol.: 8 / Source method: obtained synthetically
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


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


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#10: 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
#11: 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
#12: 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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.4 Å3/Da / Density % sol: 63.85 %
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 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 38037 / % possible obs: 98.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 73.58 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.098 / Net I/σ(I): 8.15
Reflection shellResolution: 2.6→2.67 Å / Mean I/σ(I) obs: 1.02 / Num. unique obs: 2832 / CC1/2: 0.586 / Rrim(I) all: 1.34 / % possible all: 99.3

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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: 2.6→41.99 Å / SU ML: 0.4229 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.9856
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2493 1519 4 %
Rwork0.1927 36482 -
obs0.195 38001 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.07 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6543 0 776 21 7340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00877612
X-RAY DIFFRACTIONf_angle_d1.159410371
X-RAY DIFFRACTIONf_chiral_restr0.05961041
X-RAY DIFFRACTIONf_plane_restr0.00911261
X-RAY DIFFRACTIONf_dihedral_angle_d17.29172709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.40011380.4043296X-RAY DIFFRACTION98.93
2.68-2.780.3151370.30733308X-RAY DIFFRACTION98.97
2.78-2.890.32831380.26293313X-RAY DIFFRACTION99.08
2.89-3.020.30581380.23083316X-RAY DIFFRACTION98.8
3.02-3.180.28931370.22643284X-RAY DIFFRACTION98.84
3.18-3.380.31981380.22543321X-RAY DIFFRACTION98.86
3.38-3.640.23071390.18193333X-RAY DIFFRACTION99.09
3.64-4.010.24131360.17193265X-RAY DIFFRACTION97.76
4.01-4.590.2461330.1663211X-RAY DIFFRACTION95.38
4.59-5.780.21691410.17483374X-RAY DIFFRACTION99.74
5.78-41.990.22281440.17713461X-RAY DIFFRACTION99.64

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