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- PDB-5o5w: Molybdenum storage protein room-temperature structure determined ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o5w | ||||||
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Title | Molybdenum storage protein room-temperature structure determined by serial millisecond crystallography | ||||||
![]() | (Molybdenum storage protein subunit ...) x 2 | ||||||
![]() | HYDROLASE / room-temperature / serial crystallography | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Steffen, B. / Weinert, T. / Ermler, U. / Standfuss, J. | ||||||
![]() | ![]() Title: Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons. Authors: Weinert, T. / Olieric, N. / Cheng, R. / Brunle, S. / James, D. / Ozerov, D. / Gashi, D. / Vera, L. / Marsh, M. / Jaeger, K. / Dworkowski, F. / Panepucci, E. / Basu, S. / Skopintsev, P. / ...Authors: Weinert, T. / Olieric, N. / Cheng, R. / Brunle, S. / James, D. / Ozerov, D. / Gashi, D. / Vera, L. / Marsh, M. / Jaeger, K. / Dworkowski, F. / Panepucci, E. / Basu, S. / Skopintsev, P. / Dore, A.S. / Geng, T. / Cooke, R.M. / Liang, M. / Prota, A.E. / Panneels, V. / Nogly, P. / Ermler, U. / Schertler, G. / Hennig, M. / Steinmetz, M.O. / Wang, M. / Standfuss, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.9 KB | Display | ![]() |
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PDB format | ![]() | 89.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5njmC ![]() 5nlxC ![]() 5nm2C ![]() 5nm4C ![]() 5nm5C ![]() 5nqtC ![]() 5nquC ![]() 4f6tS 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 on special symmetry positions |
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Components
-Molybdenum storage protein subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 29376.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 28378.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 6 types, 205 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/8M0.gif)
![](data/chem/img/M10.gif)
![](data/chem/img/MO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/8M0.gif)
![](data/chem/img/M10.gif)
![](data/chem/img/MO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ATP / | ||||||
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#4: Chemical | ChemComp-MG / | ||||||
#5: Chemical | #6: Chemical | ChemComp-M10 / ( | #7: Chemical | ChemComp-MO / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0,1 M Na-Citrat pH 5,6 1,4 M NH4H2PO4 20 % Glycerol |
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→24.2 Å / Num. obs: 110141 / % possible obs: 100 % / Redundancy: 765.4 % / Biso Wilson estimate: 29.42 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.29 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4F6T Resolution: 1.7→24.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.067 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.07 / SU Rfree Cruickshank DPI: 0.07
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Displacement parameters | Biso mean: 45 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.7→24.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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