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Yorodumi- PDB-5k3f: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - His... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k3f | ||||||
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Title | Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - His280Asn/Fluoroacetate - Cocrystallized - Single Protomer Reacted with Ligand | ||||||
Components | (Fluoroacetate dehalogenaseHaloacetate dehalogenase) x 2 | ||||||
Keywords | HYDROLASE / Homodimer / Dehalogenase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.54 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 | 5k3f.cif.gz | 149 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k3f.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 5k3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/5k3f ftp://data.pdbj.org/pub/pdb/validation_reports/k3/5k3f | HTTPS FTP |
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-Related structure data
Related structure data | 5k3aC 5k3bC 5k3cC 5k3dC 5k3eC 5swnC 5t4tC 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: 34107.652 Da / Num. of mol.: 1 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 |
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#2: Protein | Mass: 34049.617 Da / Num. of mol.: 1 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 |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 3350 19-22%, 200mM Calcium chloride, 100mM Tris HCL pH 8.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 17, 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→36.807 Å / Num. obs: 74512 / % possible obs: 92.7 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.54→1.58 Å / Rmerge(I) obs: 0.214 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3R3U Resolution: 1.54→36.807 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.46 Å2 / Biso mean: 15.7044 Å2 / Biso min: 4.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.54→36.807 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
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