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- PDB-3dtr: E(L212)Q, L(L227)F double mutant structure of photosynthetic reac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dtr | ||||||
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Title | E(L212)Q, L(L227)F double mutant structure of photosynthetic reaction center from Rhodobacter sphaeroides | ||||||
![]() | (Reaction center protein ...) x 3 | ||||||
![]() | PHOTOSYNTHESIS / Mutant photosynthetic reaction center / Phenotypic revertant / Proton transfer / 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 / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pokkuluri, P.R. / Schiffer, M. | ||||||
![]() | ![]() Title: Restoring proton transfer in L212Q mutant of photosynthetic reaction center Authors: Pokkuluri, P.R. / Laible, P.D. / Hanson, D.K. / 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 | ![]() | 204.2 KB | Display | ![]() |
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PDB format | ![]() | 157 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 43.8 KB | Display | |
Data in CIF | ![]() | 56 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dtaC ![]() 1k6lS C: citing same article ( 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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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: 31379.420 Da / Num. of mol.: 1 / Mutation: E(L212)Q, L(L227)F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 35365.559 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, 153 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/LDA.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 | #7: Chemical | ChemComp-LDA / #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: 5.77 Å3/Da / Density % sol: 78.77 % |
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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: Jun 8, 2004 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 36750 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3257 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1K6L with the two mutation sites changed as follows: L212Glu changed to Gln (just atom NE2 changed to OE2 kept the same coordinates) and L227Leu changed to Ala by truncating the sidechain at CB Resolution: 3.1→20 Å / σ(F): 2 / 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→20 Å
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