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Yorodumi- PDB-6gxd: The hit-and-return system enables efficient time-resolved serial ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gxd | ||||||
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Title | The hit-and-return system enables efficient time-resolved serial synchrotron crystallography: FAcD752MS after reaction initiation | ||||||
Components | fluoroacetate dehalogenase | ||||||
Keywords | DNA BINDING PROTEIN / time-resolved crystallography / serial synchrotron crystallography (SSX) / Pump-probe experiment / structural enzymology | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Schulz, E.C. / Mehrabi, P. / Mueller-Werkmeister, H. / Tellkamp, F. / Stuart, W. / Persch, E. / De Gasparo, R. / Diederich, F. / Pai, E.F. / Miller, R.J.D. | ||||||
Citation | Journal: Nat. Methods / Year: 2018 Title: The hit-and-return system enables efficient time-resolved serial synchrotron crystallography. Authors: Schulz, E.C. / Mehrabi, P. / Muller-Werkmeister, H.M. / Tellkamp, F. / Jha, A. / Stuart, W. / Persch, E. / De Gasparo, R. / Diederich, F. / Pai, E.F. / Miller, R.J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gxd.cif.gz | 142.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gxd.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 6gxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gxd_validation.pdf.gz | 722.4 KB | Display | wwPDB validaton report |
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Full document | 6gxd_full_validation.pdf.gz | 733.1 KB | Display | |
Data in XML | 6gxd_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 6gxd_validation.cif.gz | 42.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/6gxd ftp://data.pdbj.org/pub/pdb/validation_reports/gx/6gxd | HTTPS FTP |
-Related structure data
Related structure data | 6fsxC 6gxfC 6gxhC 6gxlC 6gxtC 3r3uS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 34073.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1 #2: Chemical | ChemComp-FAH / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.65 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: PEG 3350, 18-20 (w/v) CaCl2, 100 mM Tris HCl, 100 mM pH 8.5 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0089 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0089 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→81.5 Å / Num. obs: 48357 / % possible obs: 99.9 % / Redundancy: 39.5 % / Biso Wilson estimate: 18.74 Å2 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.8→1.83 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3r3u Resolution: 1.8→40.724 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 4.99 / Phase error: 20.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→40.724 Å
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Refine LS restraints |
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LS refinement shell |
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