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- PDB-1yf6: Structure of a quintuple mutant of photosynthetic reaction center... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yf6 | ||||||
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Title | Structure of a quintuple mutant of photosynthetic reaction center from rhodobacter sphaeroides | ||||||
![]() | (Reaction center protein ...) x 3 | ||||||
![]() | PHOTOSYNTHESIS / BACTERIAL PHOTOSYNTHESIS / RHODOBACTER SPHAEROIDES / GATED ELECTRON TRANSFER / QUINONE MOVEMENT / INTEGRAL MEMBRANE PROTEIN | ||||||
Function / homology | ![]() : / 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 / membrane => GO:0016020 / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Paddock, M.L. / Chang, C. / Xu, Q. / Abresch, E.C. / Axelrod, H.L. | ||||||
![]() | ![]() Title: Quinone (Q(B)) Reduction by B-Branch Electron Transfer in Mutant Bacterial Reaction Centers from Rhodobacter sphaeroides: Quantum Efficiency and X-ray Structure. Authors: Paddock, M.L. / Chang, C. / Xu, Q. / Abresch, E.C. / Axelrod, H.L. / Feher, G. / Okamura, M.Y. #1: ![]() Title: X-Ray Structure Determination of Three Mutants of the Bacterial Photosynthetic Reaction Centers from Rb. Sphaeroides; Altered Proton Transfer Pathways Authors: Xu, Q. / Axelrod, H.L. / Abresch, E.C. / Paddock, M.L. / Okamura, M.Y. / Feher, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.6 KB | Display | ![]() |
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PDB format | ![]() | 158 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.4 MB | Display | ![]() |
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Full document | ![]() | 3.5 MB | Display | |
Data in XML | ![]() | 44 KB | Display | |
Data in CIF | ![]() | 58.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rzhS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Reaction center protein ... , 3 types, 3 molecules LMH
#1: Protein | Mass: 31362.389 Da / Num. of mol.: 1 / Mutation: L181Y Source method: isolated from a genetically manipulated source Details: L181Y / Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 34580.699 Da / Num. of mol.: 1 / Mutation: M203D, M210F, M214H, M260W Source method: isolated from a genetically manipulated source Details: M203D, M210F, M214H, M260W / Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 28066.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 12 types, 384 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/SPO.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/SPO.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-BCL / #5: Chemical | ChemComp-BPH / | #6: Chemical | #7: Chemical | ChemComp-HTO / | #8: Chemical | #9: Chemical | ChemComp-GOL / | #10: Chemical | ChemComp-FE2 / | #11: Chemical | ChemComp-CL / | #12: Chemical | #13: Chemical | ChemComp-SPO / | #14: Chemical | ChemComp-CDL / | #15: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.25 Å3/Da / Density % sol: 76.4 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: POTASSIUM PHOSPHATE, SODIUM CHLORIDE, HAPTANETRIOL, DIOXANE, HAXANETRIOL, LDAO, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→39.34 Å / Num. all: 84130 / Num. obs: 84139 / % possible obs: 84.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.3 Å2 / Rsym value: 0.091 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.393 / % possible all: 70.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RZH Resolution: 2.25→39.34 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2952289.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.8034 Å2 / ksol: 0.337419 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→39.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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