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- PDB-7p17: F(M197)H mutant structure of Photosynthetic Reaction Center From ... -

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Basic information

Entry
Database: PDB / ID: 7p17
TitleF(M197)H mutant structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV by fixed-target serial synchrotron crystallography (room temperature, 12keV)
Components(Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS / Photosynthetic reaction center / bacteriochlorophyll / Rhodobacter sphaeroides / serial crystallography / 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, 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 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, 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. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / PENTADECANE / Chem-NKP / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / SPEROIDENONE / UBIQUINONE-10 / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsGabdulkhakov, A.G. / Selikhanov, G.K. / Guenther, S. / Meents, A. / Fufina, T.Y. / Vasilieva, L.G.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-02-40008_mega Russian Federation
CitationJournal: To Be Published
Title: X-Ray structure of Rhodobacter sphaeroides reaction center with M197 Phe-His substitution clarifies properties of the mutant complex
Authors: Gabdulkhakov, A.G. / Selikhanov, G.K. / Guenther, S. / Meents, A. / Fufina, T.Y. / Vasilieva, L.G.
History
DepositionJul 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / 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)101,19122
Polymers91,6533
Non-polymers9,53919
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36640 Å2
ΔGint-215 kcal/mol
Surface area28820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.500, 102.500, 237.400
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.) Rhodobacter sphaeroides (bacteria) / Gene: puhA / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain (production host): RV / References: UniProt: P0C0Y7
#2: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 31360.416 Da / Num. of mol.: 1 / Mutation: S178T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufL / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain (production host): RV / References: UniProt: P0C0Y8
#3: 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.) Rhodobacter sphaeroides (bacteria) / Gene: pufM / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain (production host): RV / References: UniProt: P0C0Y9

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Non-polymers , 11 types, 171 molecules

#4: Chemical
ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H32
#5: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#6: 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
#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-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
#10: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4
#11: Chemical ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2
#12: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#13: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 63.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
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: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.22→47.05 Å / Num. obs: 63262 / % possible obs: 99.9 % / Redundancy: 7.8 % / Biso Wilson estimate: 41.83 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.341 / Net I/σ(I): 5
Reflection shellResolution: 2.22→2.27 Å / Redundancy: 8.3 % / Rmerge(I) obs: 2.24 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4392 / CC1/2: 0.339 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6z1j

6z1j


Resolution: 2.22→47.05 Å / SU ML: 0.2743 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0544
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2148 3163 5 %
Rwork0.1766 60067 -
obs0.1785 63230 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.77 Å2
Refinement stepCycle: LAST / Resolution: 2.22→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6481 0 680 152 7313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00737722
X-RAY DIFFRACTIONf_angle_d0.970510569
X-RAY DIFFRACTIONf_chiral_restr0.15011059
X-RAY DIFFRACTIONf_plane_restr0.00751303
X-RAY DIFFRACTIONf_dihedral_angle_d23.34822725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.250.331340.29522553X-RAY DIFFRACTION99.89
2.25-2.290.30121260.26592598X-RAY DIFFRACTION99.85
2.29-2.330.31161230.24952581X-RAY DIFFRACTION99.89
2.33-2.370.31781380.24252555X-RAY DIFFRACTION99.85
2.37-2.410.27381400.23252567X-RAY DIFFRACTION99.93
2.41-2.460.27411220.23372593X-RAY DIFFRACTION99.89
2.46-2.510.30441290.22692582X-RAY DIFFRACTION100
2.51-2.560.2511470.22042577X-RAY DIFFRACTION99.82
2.56-2.620.29141290.20842576X-RAY DIFFRACTION99.89
2.62-2.680.27251430.21592588X-RAY DIFFRACTION99.93
2.69-2.760.27711190.20622606X-RAY DIFFRACTION99.96
2.76-2.840.23571400.19252594X-RAY DIFFRACTION99.89
2.84-2.930.25861360.18062599X-RAY DIFFRACTION99.89
2.93-3.040.21261340.16852579X-RAY DIFFRACTION99.78
3.04-3.160.2091500.1652587X-RAY DIFFRACTION99.64
3.16-3.30.21671450.16072618X-RAY DIFFRACTION99.78
3.3-3.470.20091560.15312579X-RAY DIFFRACTION99.89
3.47-3.690.18411470.14782629X-RAY DIFFRACTION99.93
3.69-3.980.16741520.14252618X-RAY DIFFRACTION99.71
3.98-4.380.18371410.14492637X-RAY DIFFRACTION99.89
4.38-5.010.1811280.15282694X-RAY DIFFRACTION99.82
5.01-6.310.21411400.18452705X-RAY DIFFRACTION99.3
6.31-47.050.18291440.17412852X-RAY DIFFRACTION98.46

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