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- PDB-3dts: E(L212)A, D(L213)A, R(M233)L triple mutant structure of photosynt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dts | ||||||
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Title | E(L212)A, D(L213)A, R(M233)L triple mutant structure of photosynthetic reaction center from Rhodobacter sphaeroides | ||||||
![]() | (Reaction center protein ...![]() | ||||||
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Function / homology | ![]() plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pokkuluri, P.R. / Schiffer, M. | ||||||
![]() | ![]() Title: Structural description of compensatory mutations that restore proton transfer pathways to the L212-L213A mutant bacterial reaction center Authors: Pokkuluri, P.R. / Laible, P.D. / K Hanson, D. / Schiffer, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.7 KB | Display | ![]() |
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PDB format | ![]() | 157.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1k6lS 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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1 |
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Unit cell |
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Details | Authors state that the photosynthetic reaction center is a complex made up of three protein chains (L,M,H) and several co-factors. |
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Components
-Reaction center protein ... , 3 types, 3 molecules LMH
#1: Protein | ![]() Mass: 31244.346 Da / Num. of mol.: 1 / Mutation: E(L212)A, D(L213)A, R(M233)L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 35321.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source 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 , 8 types, 103 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-BCL / ![]() #5: Chemical | ![]() #6: Chemical | ChemComp-LDA / ![]() #7: Chemical | ![]() #8: Chemical | ChemComp-FE / | ![]() #9: Chemical | ChemComp-SPN / | #10: Chemical | ChemComp-CDL / | ![]() #11: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.87 Å3/Da / Density % sol: 79.05 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Potassium phosphate, LDAO, Heptane triol, Dioxane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 18, 2003 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.1→30 Å / Num. obs: 32158 / % possible obs: 85 % / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2504 / % possible all: 73 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1K6L with the three mutation sites changed as follows: L212Glu, L213Asp and M233Arg were changed to Alanines by truncating their sidechains at CB Resolution: 3.1→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: After refitting, only isotropic B-factor refinement was done with CNS. No positional refinement was done
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Refinement step | Cycle: LAST / Resolution: 3.1→30 Å
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