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- PDB-5v33: R. sphaeroides photosythetic reaction center mutant - Residue L22... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5v33 | ||||||
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Title | R. sphaeroides photosythetic reaction center mutant - Residue L223, Ser to Trp - Room Temperature Structure Solved on X-ray Transparent Microfluidic Chip | ||||||
![]() | (Reaction center protein ...) x 3 | ||||||
![]() | PHOTOSYNTHESIS / reaction center mutant | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Schieferstein, J.M. / Pawate, A.S. / Sun, C. / Wan, F. / Broecker, J. / Ernst, O.P. / Gennis, R.B. / Kenis, P.J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray transparent microfluidic chips for high-throughput screening and optimization of in meso membrane protein crystallization. Authors: Schieferstein, J.M. / Pawate, A.S. / Sun, C. / Wan, F. / Sheraden, P.N. / Broecker, J. / Ernst, O.P. / Gennis, R.B. / Kenis, P.J.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 | ![]() | 357.6 KB | Display | ![]() |
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PDB format | ![]() | 289.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 32.5 KB | Display | |
Data in CIF | ![]() | 42.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4tqqS 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: 26022.904 Da / Num. of mol.: 1 / Fragment: UNP residues 11-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 31445.521 Da / Num. of mol.: 1 / Mutation: S223W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 33871.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 4 types, 8 molecules ![](data/chem/img/BPH.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/U10.gif)
#4: Chemical | #5: Chemical | ChemComp-BCL / #6: Chemical | ChemComp-FE / | #7: Chemical | ChemComp-U10 / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.29 % |
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Crystal grow | Temperature: 293 K / Method: microfluidic / pH: 7.8 Details: Crystals were grown in microfluidic wells. LCPs were formulated by overlaying ~40 nl of protein solution over ~10 nl of solid monoolein. LCPs formed by diffusion during a 4 hour incubation. ...Details: Crystals were grown in microfluidic wells. LCPs were formulated by overlaying ~40 nl of protein solution over ~10 nl of solid monoolein. LCPs formed by diffusion during a 4 hour incubation. Precipitants were then introduced to the crystallization well, and crystals were observed after 3 days. Crystals were grown at 15-20 mg/mL protein concentration (in 10 mM Tris pH 7.8, 280 mM NaCl, 0.05% LDAO) with a precipitant of 1 M HEPES pH 7.5, 1.15 M (NH4)2(SO4) and 14-15 %w/v Jeffamine M-600. |
-Data collection
Diffraction | Mean temperature: 298 K / Ambient temp details: Room temperature | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.5→50 Å / Num. obs: 15671 / % possible obs: 92 % / Redundancy: 5.4 % / Biso Wilson estimate: 54.65 Å2 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.132 / Rrim(I) all: 0.322 / Χ2: 0.926 / Net I/σ(I): 2.9 / Num. measured all: 84779 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4TQQ Resolution: 3.487→47.076 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.41 Å2 / Biso mean: 45.5477 Å2 / Biso min: 24.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.487→47.076 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 12.1594 Å / Origin y: -28.4138 Å / Origin z: -33.9378 Å
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Refinement TLS group |
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