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Yorodumi- PDB-5o5w: Molybdenum storage protein room-temperature structure determined ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o5w | ||||||
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Title | Molybdenum storage protein room-temperature structure determined by serial millisecond crystallography | ||||||
Components | (Molybdenum storage protein subunit ...) x 2 | ||||||
Keywords | HYDROLASE / room-temperature / serial crystallography | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Azotobacter vinelandii DJ (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Steffen, B. / Weinert, T. / Ermler, U. / Standfuss, J. | ||||||
Citation | Journal: Nat Commun / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o5w.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o5w.ent.gz | 89.6 KB | Display | PDB format |
PDBx/mmJSON format | 5o5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/5o5w ftp://data.pdbj.org/pub/pdb/validation_reports/o5/5o5w | HTTPS FTP |
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-Related structure data
Related structure data | 5njmC 5nlxC 5nm2C 5nm4C 5nm5C 5nqtC 5nquC 4f6tS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Azotobacter vinelandii DJ (bacteria) / Gene: mosA, Avin_43200 / Production host: Escherichia coli (E. coli) / References: UniProt: P84308 |
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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.) Azotobacter vinelandii DJ (bacteria) / Gene: mosB, Avin_43210 / Production host: Escherichia coli (E. coli) / References: UniProt: P84253 |
-Non-polymers , 6 types, 205 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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