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Yorodumi- PDB-5swn: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5swn | ||||||
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Title | Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Fluoroacetate - Cocrystallized | ||||||
Components | Fluoroacetate dehalogenase | ||||||
Keywords | HYDROLASE / Homodimer / Dehalogenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.541 Å | ||||||
Authors | Mehrabi, P. / Kim, T.H. / Prosser, S.R. / Pai, E.F. | ||||||
Citation | Journal: Science / Year: 2017 Title: The role of dimer asymmetry and protomer dynamics in enzyme catalysis. Authors: Kim, T.H. / Mehrabi, P. / Ren, Z. / Sljoka, A. / Ing, C. / Bezginov, A. / Ye, L. / Pomes, R. / Prosser, R.S. / 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 | 5swn.cif.gz | 141 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5swn.ent.gz | 108.1 KB | Display | PDB format |
PDBx/mmJSON format | 5swn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/5swn ftp://data.pdbj.org/pub/pdb/validation_reports/sw/5swn | HTTPS FTP |
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-Related structure data
Related structure data | 5k3aC 5k3bC 5k3cC 5k3dC 5k3eC 5k3fC 5t4tC 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: 33221.754 Da / Num. of mol.: 2 / Mutation: D110N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic) Strain: ATCC BAA-98 / CGA009 / Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase #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: 2.05 Å3/Da / Density % sol: 40.14 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris-HCl pH 8.5 and 200 mM CaCl2 and 19-22% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→40.8 Å / Num. obs: 78560 / % possible obs: 99.1 % / Redundancy: 4.6 % / Rsym value: 0.034 / Net I/σ(I): 30.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3r3u Resolution: 1.541→40.777 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.541→40.777 Å
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Refine LS restraints |
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LS refinement shell |
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