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Yorodumi- PDB-6qi1: Time resolved structural analysis of the full turnover of an enzy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qi1 | ||||||
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Title | Time resolved structural analysis of the full turnover of an enzyme - 12312 ms | ||||||
Components | Fluoroacetate dehalogenaseHaloacetate dehalogenase | ||||||
Keywords | HYDROLASE / time-resolved / catalysis / intermediate | ||||||
Function / homology | Function and homology information haloacetate dehalogenase / haloacetate dehalogenase activity / epoxide hydrolase activity Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Schulz, E.C. / Mehrabi, P. / Pai, E.F. / Miller, D. | ||||||
Citation | Journal: Science / Year: 2019 Title: Time-resolved crystallography reveals allosteric communication aligned with molecular breathing. Authors: Mehrabi, P. / Schulz, E.C. / Dsouza, R. / Muller-Werkmeister, H.M. / Tellkamp, F. / Miller, R.J.D. / Pai, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qi1.cif.gz | 134.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qi1.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 6qi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/6qi1 ftp://data.pdbj.org/pub/pdb/validation_reports/qi/6qi1 | HTTPS FTP |
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-Related structure data
Related structure data | 6qhpC 6qhqC 6qhsC 6qhtC 6qhuC 6qhvC 6qhwC 6qhxC 6qhyC 6qhzC 6qi0C 6qi2C 6qi3C 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 (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: 38.74 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: 18-20 % (w/v)) PEG3350, 200 mM CaCl2, and 100 mM Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9627 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: 0.9627 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→82.32 Å / Num. obs: 42453 / % possible obs: 99.9 % / Redundancy: 31.1 % / Net I/σ(I): 2.1 |
Reflection shell | Resolution: 1.9→1.94 Å |
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Resolution: 1.9→20.048 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20.048 Å
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Refine LS restraints |
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LS refinement shell |
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