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- PDB-8c3f: Double mutant I(L177)H/F(M197)H structure of Photosynthetic React... -

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Basic information

Entry
Database: PDB / ID: 8c3f
TitleDouble mutant I(L177)H/F(M197)H structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV
Components(Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS / Photosynthetic reaction center / bacteriochlorophyll / Rhodobacter sphaeroides / 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 B / CARDIOLIPIN / 1,4-DIETHYLENE DIOXIDE / : / HEPTANE-1,2,3-TRIOL / : / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-10 ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN B / CARDIOLIPIN / 1,4-DIETHYLENE DIOXIDE / : / HEPTANE-1,2,3-TRIOL / : / 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: 2.6 Å
AuthorsGabdulkhakov, A.G. / Selikhanov, G.K. / Fufina, T.Y. / Vasilieva, L.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Membranes (Basel) / Year: 2023
Title: Properties and Crystal Structure of the Cereibacter sphaeroides Photosynthetic Reaction Center with Double Amino Acid Substitution I(L177)H + F(M197)H.
Authors: Fufina, T.Y. / Selikhanov, G.K. / Gabdulkhakov, A.G. / Vasilieva, L.G.
History
DepositionDec 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,12040
Polymers91,5913
Non-polymers12,52937
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43370 Å2
ΔGint-217 kcal/mol
Surface area27910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.346, 139.346, 184.574
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 LMH

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


Mass: 31385.404 Da / Num. of mol.: 1 / Mutation: S178T, I177H
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) / Strain (production host): RV / References: UniProt: P0C0Y8
#2: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34008.090 Da / Num. of mol.: 1 / Mutation: S8T, F197H
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
#3: Protein Reaction center protein H chain / Photosynthetic reaction center H subunit


Mass: 26197.102 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

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Non-polymers , 16 types, 148 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


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


Mass: 148.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16O3
#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-BPB / BACTERIOPHEOPHYTIN B


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: 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
#10: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#11: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#12: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#13: 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
#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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#16: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#17: 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
#18: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 5.65 Å3/Da / Density % sol: 78.22 %
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, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03312 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03312 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 64208 / % possible obs: 99.7 % / Redundancy: 9.9 % / Biso Wilson estimate: 63.04 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.2
Reflection shellResolution: 2.6→2.67 Å / Rmerge(I) obs: 2.16 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 4564 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V3Z

3v3z


Resolution: 2.6→46.12 Å / SU ML: 0.3888 / Cross valid method: FREE R-VALUE / σ(F): 0.23 / Phase error: 26.631
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2198 5901 4.79 %
Rwork0.1943 117402 -
obs0.1955 64207 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.95 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 0 829 111 7405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087546
X-RAY DIFFRACTIONf_angle_d1.147710289
X-RAY DIFFRACTIONf_chiral_restr0.05341022
X-RAY DIFFRACTIONf_plane_restr0.00891249
X-RAY DIFFRACTIONf_dihedral_angle_d18.10912676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.38882000.34923995X-RAY DIFFRACTION100
2.63-2.660.3632460.33443830X-RAY DIFFRACTION99.95
2.66-2.690.37031700.33433935X-RAY DIFFRACTION99.98
2.69-2.730.37221960.3193858X-RAY DIFFRACTION100
2.73-2.760.37122080.30263937X-RAY DIFFRACTION100
2.76-2.80.31781840.30953881X-RAY DIFFRACTION99.95
2.8-2.840.35751660.29053998X-RAY DIFFRACTION99.93
2.84-2.880.29012100.27783891X-RAY DIFFRACTION100
2.88-2.930.30042160.26953920X-RAY DIFFRACTION100
2.93-2.980.29771960.26323899X-RAY DIFFRACTION99.98
2.98-3.030.25271860.25493897X-RAY DIFFRACTION100
3.03-3.080.30022180.25243899X-RAY DIFFRACTION100
3.08-3.140.22831900.24283891X-RAY DIFFRACTION100
3.14-3.210.29551920.23773935X-RAY DIFFRACTION100
3.21-3.280.26862440.21893868X-RAY DIFFRACTION100
3.28-3.350.2461720.19543967X-RAY DIFFRACTION99.88
3.35-3.440.16612020.18823878X-RAY DIFFRACTION100
3.44-3.530.22891400.1863959X-RAY DIFFRACTION100
3.53-3.630.22381890.18053897X-RAY DIFFRACTION100
3.63-3.750.20811620.17753983X-RAY DIFFRACTION100
3.75-3.880.19792280.17483858X-RAY DIFFRACTION100
3.88-4.040.20481960.15873914X-RAY DIFFRACTION100
4.04-4.220.19752020.15913955X-RAY DIFFRACTION99.98
4.22-4.440.15661620.15353926X-RAY DIFFRACTION100
4.45-4.720.17051900.15643900X-RAY DIFFRACTION100
4.72-5.090.16391930.15993908X-RAY DIFFRACTION100
5.09-5.60.1721900.16783936X-RAY DIFFRACTION100
5.6-6.410.20162080.17143912X-RAY DIFFRACTION100
6.41-8.050.16592320.16423856X-RAY DIFFRACTION100
8.07-46.120.24842130.19993919X-RAY DIFFRACTION99.81

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