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Yorodumi- PDB-8c6k: Double mutant A(L53)C/I(L64)C structure of Photosynthetic Reactio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c6k | ||||||
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Title | Double mutant A(L53)C/I(L64)C structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV | ||||||
Components | (Reaction center protein ...Photosynthetic reaction centre) x 3 | ||||||
Keywords | PHOTOSYNTHESIS / 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 / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / metal ion binding Similarity search - Function | ||||||
Biological species | Cereibacter sphaeroides 2.4.1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.86 Å | ||||||
Authors | Gabdulkhakov, A. / Selikhanov, G. / Fufina, T. / Vasilieva, L. / Atamas, A. / Uhimchuk, D. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c6k.cif.gz | 420.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c6k.ent.gz | 291.6 KB | Display | PDB format |
PDBx/mmJSON format | 8c6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/8c6k ftp://data.pdbj.org/pub/pdb/validation_reports/c6/8c6k | HTTPS FTP |
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-Related structure data
Related structure data | 8c5xC 8c7cC 8c87C 8c88C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Reaction center protein ... , 3 types, 3 molecules HLM
#1: Protein | 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 |
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#2: Protein | 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 | 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 |
-Non-polymers , 14 types, 72 molecules
#4: Chemical | ChemComp-LDA / #5: Chemical | ChemComp-UNL / Num. of mol.: 10 / Source method: obtained synthetically #6: Chemical | #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-K / | #9: Chemical | ChemComp-BCL / #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-DIO / | #13: Chemical | #14: Chemical | ChemComp-CDL / | #15: Chemical | ChemComp-FE / | #16: Chemical | ChemComp-SPN / | #17: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.68 Å3/Da / Density % sol: 78.35 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Oct 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.86→29.89 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 45.3796682255 Å / Origin y: 41.1550626899 Å / Origin z: 27.4308441818 Å
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1
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