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Open data
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Basic information
Entry | Database: PDB / ID: 1z9j | ||||||
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Title | Photosynthetic Reaction Center from Rhodobacter sphaeroides | ||||||
![]() | (Reaction center protein ...![]() | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thielges, M. / Uyeda, G. / Camara-Artigas, A. / Kalman, L. / Williams, J.C. / Allen, J.P. | ||||||
![]() | ![]() Title: Design of a Redox-Linked Active Metal Site: Manganese Bound to Bacterial Reaction Centers at a Site Resembling That of Photosystem II Authors: Thielges, M. / Uyeda, G. / Camara-Artigas, A. / Kalman, L. / Williams, J.C. / Allen, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171 KB | Display | ![]() |
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PDB format | ![]() | 128.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1z9kC ![]() 1m3xS S: Starting model for refinement C: citing same article ( |
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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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Components
-Reaction center protein ... , 3 types, 3 molecules ABC
#1: Protein | ![]() Mass: 31371.377 Da / Num. of mol.: 1 / Mutation: L131H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 34476.438 Da / Num. of mol.: 1 / Mutation: L160H, R164Y, M168E, F197H, G288D 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 , 6 types, 12 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-BCL / ![]() #5: Chemical | ![]() #6: Chemical | ![]() #7: Chemical | ChemComp-FE / | ![]() #8: Chemical | ChemComp-MN / | #9: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.3 Å3/Da / Density % sol: 80 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG,NaCl,MnCl, LDAO, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 8, 2003 / Details: graphite |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 4.5→25 Å / Num. all: 65241 / Num. obs: 13804 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 120 Å2 / Rmerge(I) obs: 0.19 / Rsym value: 0.17 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 4.5→4.8 Å / Rmerge(I) obs: 0.86 / % possible all: 92 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1m3x Resolution: 4.5→19.96 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 4332507.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 283.89 Å2 / ksol: 0.646587 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 4.5→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.5→4.78 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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