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- PDB-2gmr: Photosynthetic reaction center mutant from Rhodobacter sphaeroide... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gmr | ||||||
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Title | Photosynthetic reaction center mutant from Rhodobacter sphaeroides with Asp L210 replaced with Asn | ||||||
![]() | (Photosynthetic 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 | ![]() ![]() ![]() | ||||||
![]() | Stachnik, J.M. / Hermes, S. / Gerwert, K. / Hofmann, E. | ||||||
![]() | ![]() Title: Proton uptake in the reaction center mutant L210DN from Rhodobacter sphaeroides via protonated water molecules. Authors: Hermes, S. / Stachnik, J.M. / Onidas, D. / Remy, A. / Hofmann, E. / Gerwert, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200.3 KB | Display | ![]() |
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PDB format | ![]() | 155 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1aigS 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 | biological unit is a trimer chains L, M, H |
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Components
-Photosynthetic Reaction center protein ... , 3 types, 3 molecules LMH
#1: Protein | ![]() Mass: 31345.404 Da / Num. of mol.: 1 / Mutation: L210DN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 34398.543 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 , 7 types, 194 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-BCL / ![]() #5: Chemical | ![]() #6: Chemical | ![]() #7: Chemical | ChemComp-LDA / ![]() #8: Chemical | ChemComp-FE2 / | #9: Chemical | ChemComp-SPN / | #10: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.51 % |
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Crystal grow![]() | Temperature: 301 K / pH: 8 Details: 20% PEG 4000, 100mM Tris-Cl, 750mM NaCl, 3% 1,2,3-heptanetriole, 0.12% LDAO, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 301.0K, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→38.433 Å / Num. obs: 50281 / % possible obs: 97.4 % / Biso Wilson estimate: 31.4 Å2 / Rsym value: 0.056 / Net I/σ(I): 24.49 |
Reflection shell | Resolution: 2.5→2.6 Å / Mean I/σ(I) obs: 6.35 / Rsym value: 0.334 / % possible all: 99.3 |
-Phasing
Phasing MR | Rfactor: 0.387 / Cor.coef. Fo:Fc: 0.679
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1AIG Resolution: 2.5→38.43 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.3344 Å2 / ksol: 0.308988 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→38.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rwork: 0.25 / Total num. of bins used: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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