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- PDB-7p2c: F(M197)H mutant structure of Photosynthetic Reaction Center From ... -

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Basic information

Entry
Database: PDB / ID: 7p2c
TitleF(M197)H mutant structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV by fixed-target serial synchrotron crystallography (room temperature, 26keV)
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, 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 A / : / PENTADECANE / Chem-NKP / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-10 / Reaction center protein H chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / PENTADECANE / Chem-NKP / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / 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: 2.04 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: Iucrj / Year: 2022
Title: X-ray structure of the Rhodobacter sphaeroides reaction center with an M197 Phe→His substitution clarifies the properties of the mutant complex.
Authors: Selikhanov, G. / Fufina, T. / Guenther, S. / Meents, A. / Gabdulkhakov, A. / Vasilieva, L.
History
DepositionJul 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 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

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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)101,07422
Polymers91,6533
Non-polymers9,42119
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36050 Å2
ΔGint-217 kcal/mol
Surface area29370 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 (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
Gene: puhA, RHOS4_18960, RSP_0291 / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain (production host): RV / References: UniProt: Q3J170
#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 (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
Gene: pufL, RHOS4_18610, RSP_0257 / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / References: UniProt: Q3J1A5
#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 (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
Gene: pufM, RHOS4_18600, RSP_0256 / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain (production host): RV / References: UniProt: Q3J1A6

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Non-polymers , 12 types, 193 molecules

#4: 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
#5: 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
#6: Chemical ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H32
#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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#12: Chemical ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2
#13: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#14: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 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: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.4769 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: 0.4769 Å / Relative weight: 1
ReflectionResolution: 2.04→47.05 Å / Num. obs: 81278 / % possible obs: 100 % / Redundancy: 28.7 % / Biso Wilson estimate: 36.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.306 / Net I/σ(I): 10.2
Reflection shellResolution: 2.04→2.08 Å / Rmerge(I) obs: 5.556 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4373 / CC1/2: 0.403
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: Roadrune / Sample holding: silicon chip

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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: 2.04→47.05 Å / SU ML: 0.2345 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9373
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229 4079 5.02 %
Rwork0.201 77154 -
obs0.2024 81233 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.05 Å2
Refinement stepCycle: LAST / Resolution: 2.04→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 670 174 7310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00737701
X-RAY DIFFRACTIONf_angle_d0.928810548
X-RAY DIFFRACTIONf_chiral_restr0.15061059
X-RAY DIFFRACTIONf_plane_restr0.0081303
X-RAY DIFFRACTIONf_dihedral_angle_d21.46372713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.060.33151330.31022610X-RAY DIFFRACTION99.96
2.06-2.090.3221170.30882647X-RAY DIFFRACTION99.86
2.09-2.120.32811470.28142591X-RAY DIFFRACTION99.96
2.12-2.140.25141620.26732616X-RAY DIFFRACTION99.96
2.14-2.170.30431350.27312609X-RAY DIFFRACTION100
2.17-2.20.31371500.26812616X-RAY DIFFRACTION99.96
2.2-2.240.29521430.25822611X-RAY DIFFRACTION100
2.24-2.270.27521240.2532659X-RAY DIFFRACTION100
2.27-2.310.29481300.23742629X-RAY DIFFRACTION100
2.31-2.350.29331340.22872616X-RAY DIFFRACTION99.96
2.35-2.390.25251380.22072633X-RAY DIFFRACTION99.96
2.39-2.440.24481440.21152642X-RAY DIFFRACTION100
2.44-2.490.26241260.22542644X-RAY DIFFRACTION99.96
2.49-2.540.26231320.21442636X-RAY DIFFRACTION99.96
2.54-2.60.24621460.19932626X-RAY DIFFRACTION100
2.6-2.670.24131480.1972633X-RAY DIFFRACTION100
2.67-2.740.22421230.19792664X-RAY DIFFRACTION100
2.74-2.820.20931370.18762667X-RAY DIFFRACTION100
2.82-2.910.19921430.18542645X-RAY DIFFRACTION100
2.91-3.010.20941300.18092676X-RAY DIFFRACTION100
3.01-3.130.2231640.1882621X-RAY DIFFRACTION99.96
3.13-3.280.24451400.19342686X-RAY DIFFRACTION100
3.28-3.450.22191620.17482652X-RAY DIFFRACTION100
3.45-3.660.18141500.18022689X-RAY DIFFRACTION100
3.66-3.950.19791540.17352681X-RAY DIFFRACTION100
3.95-4.340.22071450.17872705X-RAY DIFFRACTION100
4.34-4.970.19581360.18422753X-RAY DIFFRACTION100
4.97-6.260.2371400.20822779X-RAY DIFFRACTION100
6.26-47.050.21921460.20212918X-RAY DIFFRACTION98.52

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