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- PDB-3v3z: I(L177)H mutant structure of photosynthetic reaction center from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v3z | ||||||
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Title | I(L177)H mutant structure of photosynthetic reaction center from Rhodobacter sphaeroides | ||||||
![]() | (Reaction center protein ...) x 3 | ||||||
![]() | ELECTRON TRANSPORT / Photosynthetic reaction center / Primary electron donor / membrane | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Gabdulkhakov, A.G. / Fufina, T.Y. / Vasilieva, L.G. / Shuvalov, V.A. | ||||||
![]() | ![]() Title: The site-directed mutation I(L177)H in Rhodobacter sphaeroides reaction center affects coordination of P(A) and B(B) bacteriochlorophylls. Authors: Vasilieva, L.G. / Fufina, T.Y. / Gabdulkhakov, A.G. / Leonova, M.M. / Khatypov, R.A. / Shuvalov, V.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.2 KB | Display | ![]() |
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PDB format | ![]() | 154.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3v3yC ![]() 1e6dS 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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Components
-Reaction center protein ... , 3 types, 3 molecules HLM
#1: Protein | Mass: 26170.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 31385.404 Da / Num. of mol.: 1 / Mutation: I177H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 33885.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 12 types, 76 molecules ![](data/chem/img/LDA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/DIO.gif)
![](data/chem/img/K.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/DIO.gif)
![](data/chem/img/K.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-LDA / #5: Chemical | ChemComp-PO4 / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-K / | #9: Chemical | ChemComp-BCL / #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-FE / | #13: Chemical | ChemComp-SPN / | #14: Chemical | ChemComp-CL / | #15: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHORS STATE THAT THE DISCREPANC |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.77 Å3/Da / Density % sol: 78.67 % |
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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, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 24, 2011 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→28.9 Å / Num. all: 47384 / Num. obs: 45707 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.61 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.25 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.55 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.3 / % possible all: 90.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1E6D Resolution: 2.9→28.9 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 13.174 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.424 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.052 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→28.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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