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- PDB-8c6k: Double mutant A(L53)C/I(L64)C structure of Photosynthetic Reactio... -

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Basic information

Entry
Database: PDB / ID: 8c6k
TitleDouble mutant A(L53)C/I(L64)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, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / Photosynthetic reaction centre, M subunit / 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, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / Photosynthetic reaction centre, M subunit / 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 / MOLECULAR REPLACEMENT / Resolution: 2.86 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 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

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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)103,46944
Polymers91,6843
Non-polymers11,78541
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46430 Å2
ΔGint-152 kcal/mol
Surface area27830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.636, 139.636, 185.091
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: 31382.467 Da / Num. of mol.: 1 / Mutation: A53C, I64C
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: 34017.117 Da / Num. of mol.: 1
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) / References: UniProt: P0C0Y9

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Non-polymers , 14 types, 72 molecules

#4: 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
#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.: 3 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / 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.: 2 / 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.: 31 / 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: 5.68 Å3/Da / Density % sol: 78.35 %
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: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Oct 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 49267 / % possible obs: 99.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 8.9 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.27 / Net I/σ(I): 5.42
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 4765 / CC1/2: 0.59

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PHENIX1.20.1_4487refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→29.89 Å / SU ML: 0.4667 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1448
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.279 2435 5.02 %
Rwork0.2285 46065 -
obs0.231 48500 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.92 Å2
Refinement stepCycle: LAST / Resolution: 2.86→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6470 0 908 31 7409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01017679
X-RAY DIFFRACTIONf_angle_d1.314510437
X-RAY DIFFRACTIONf_chiral_restr0.05641031
X-RAY DIFFRACTIONf_plane_restr0.00941262
X-RAY DIFFRACTIONf_dihedral_angle_d18.38272763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.920.38491310.33772565X-RAY DIFFRACTION95.57
2.92-2.980.37191440.33222662X-RAY DIFFRACTION99.26
2.98-3.050.35871630.31762665X-RAY DIFFRACTION99.68
3.05-3.130.37471590.31562646X-RAY DIFFRACTION99.57
3.13-3.210.3411430.29212678X-RAY DIFFRACTION99.79
3.21-3.310.35371610.28222697X-RAY DIFFRACTION99.86
3.31-3.410.30331280.2462713X-RAY DIFFRACTION100
3.41-3.530.29791340.24692689X-RAY DIFFRACTION99.93
3.53-3.680.2761560.22852717X-RAY DIFFRACTION99.97
3.68-3.840.24561210.19772708X-RAY DIFFRACTION99.96
3.84-4.040.27691000.18442732X-RAY DIFFRACTION99.79
4.05-4.30.20161670.17282726X-RAY DIFFRACTION99.86
4.3-4.630.19751690.15352703X-RAY DIFFRACTION99.93
4.63-5.090.20071190.14922740X-RAY DIFFRACTION99.9
5.09-5.820.19781340.16072780X-RAY DIFFRACTION100
5.82-7.320.19851440.17472775X-RAY DIFFRACTION100
7.32-29.890.23861620.18422869X-RAY DIFFRACTION99.41
Refinement TLS params.Method: refined / Origin x: 45.3796682255 Å / Origin y: 41.1550626899 Å / Origin z: 27.4308441818 Å
111213212223313233
T-0.0440997904037 Å20.0560855788775 Å2-0.0646503717212 Å2--0.0420683165819 Å20.0890146334431 Å2---0.0597028240352 Å2
L0.0089848798468 °2-0.00557504273235 °20.00309566995477 °2-0.0262422777222 °2-0.0145455584845 °2---0.00820379134267 °2
S0.0283393911926 Å °-0.0110708910465 Å °-0.0474912547003 Å °0.0221542988253 Å °-0.0700176509661 Å °-0.0303408554489 Å °-0.032976292239 Å °-0.0525256194414 Å °3.91273523423E-12 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1

IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1{H|11 - 411}HA - UA11 - 4111
2{M|1 - 508}M1 - 508

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