[English] 日本語
Yorodumi- PDB-8c5x: Double mutant A(L37)C/S(L99)C structure of Photosynthetic Reactio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c5x | ||||||
---|---|---|---|---|---|---|---|
Title | Double mutant A(L37)C/S(L99)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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Gabdulkhakov, A. / Selikhanov, G. / Fufina, T. / Vasilieva, L. / Atamas, A. / Uhimchuk, D. | ||||||
Funding support | Russian Federation, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8c5x.cif.gz | 228.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8c5x.ent.gz | 161.4 KB | Display | PDB format |
PDBx/mmJSON format | 8c5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/8c5x ftp://data.pdbj.org/pub/pdb/validation_reports/c5/8c5x | HTTPS FTP |
---|
-Related structure data
Related structure data | 8c6kC 8c7cC 8c87C 8c88C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-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 |
---|---|
#2: Protein | Mass: 31408.545 Da / Num. of mol.: 1 / Mutation: A37C, S99C 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) / 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) Strain: RV / Gene: pufM / Production host: Cereibacter sphaeroides 2.4.1 (bacteria) / References: UniProt: P0C0Y9 |
-Non-polymers , 14 types, 149 molecules
#4: Chemical | ChemComp-LDA / #5: Chemical | ChemComp-UNL / Num. of mol.: 10 / Source method: obtained synthetically #6: Chemical | ChemComp-PO4 / #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-K / | #9: Chemical | ChemComp-BCL / #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-DIO / | #13: Chemical | ChemComp-HTO / | #14: Chemical | ChemComp-CDL / | #15: Chemical | ChemComp-FE / | #16: Chemical | ChemComp-SPN / | #17: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.74 Å3/Da / Density % sol: 78.58 % |
---|---|
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: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 65303 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 52.72 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.13 |
Reflection shell | Resolution: 2.6→2.67 Å / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 4784 / CC1/2: 0.57 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.89 Å / SU ML: 0.2728 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6743 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→29.89 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|