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Yorodumi- PDB-6gxt: The hit-and-return system enables efficient time-resolved serial ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gxt | ||||||
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Title | The hit-and-return system enables efficient time-resolved serial synchrotron crystallography: FAcD2052MS after reaction initiation | ||||||
Components | Fluoroacetate dehalogenaseHaloacetate dehalogenase | ||||||
Keywords | DNA BINDING PROTEIN / time-resolved crystallography / serial synchrotron crystallography (SSX) / Pump-probe experiment / structural enzymology | ||||||
Function / homology | Function and homology information haloacetate dehalogenase / haloacetate dehalogenase activity / epoxide hydrolase activity Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris CGA009 (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 | 6gxt.cif.gz | 133.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gxt.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 6gxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/6gxt ftp://data.pdbj.org/pub/pdb/validation_reports/gx/6gxt | HTTPS FTP |
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-Related structure data
Related structure data | 6fsxC 6gxdC 6gxfC 6gxhC 6gxlC 3r3uS 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
#1: Protein | Mass: 34073.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic) Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase #2: Chemical | ChemComp-FAH / | #3: 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: 2.01 Å3/Da / Density % sol: 38.69 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: PEG 3350 18 - 20 % CaCl 200 mM TrisHCL 100 mM pH 8.5 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.96269 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96269 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→57.51 Å / Num. obs: 39351 / % possible obs: 99.9 % / Redundancy: 59.2 % / Net I/σ(I): 4 |
Reflection shell | Resolution: 1.95→2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3r3u Resolution: 1.95→57.199 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 5.47 / Phase error: 23.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→57.199 Å
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Refine LS restraints |
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LS refinement shell |
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