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Yorodumi- PDB-5lbx: Structure of the T175V Etr1p mutant in the trigonal form P312 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lbx | ||||||
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Title | Structure of the T175V Etr1p mutant in the trigonal form P312 in complex with NADP and crotonyl-CoA | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADPH, B-specific] 1, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Negative catalysis / enzyme / NADP / mitochondria / mutant / crotonyl-coa / reductase | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase (NADPH) / trans-2-enoyl-CoA reductase (NADPH) activity / fatty acid metabolic process / fatty acid biosynthetic process / mitochondrion Similarity search - Function | ||||||
Biological species | Candida tropicalis (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wagner, T. / Rosenthal, R.G. / Voegeli, B. / Shima, S. / Erb, T.J. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: A conserved threonine prevents self-intoxication of enoyl-thioester reductases. Authors: Rosenthal, R.G. / Vogeli, B. / Wagner, T. / Shima, S. / Erb, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lbx.cif.gz | 299.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lbx.ent.gz | 243.2 KB | Display | PDB format |
PDBx/mmJSON format | 5lbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lbx_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5lbx_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5lbx_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 5lbx_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/5lbx ftp://data.pdbj.org/pub/pdb/validation_reports/lb/5lbx | HTTPS FTP |
-Related structure data
Related structure data | 5lb9C 4w99S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42087.160 Da / Num. of mol.: 2 / Mutation: T175V Source method: isolated from a genetically manipulated source Details: The 20 first residues are not visible in the crystal structure. The sequence corresponds to the fragment 23-386 from the original gene sequence. Source: (gene. exp.) Candida tropicalis (yeast) / Gene: ETR1 / Plasmid: pTE264 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8WZM3, EC: 1.3.1.10, trans-2-enoyl-CoA reductase (NADPH) |
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-Non-polymers , 5 types, 207 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: 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: 3.47 Å3/Da / Density % sol: 64.57 % Description: Crystals are transparent cubic shaped with a volume of approximately 50-100 micron cube |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: Etr1p was crystallized at 15 mg/mL with 5 mM NADP and 5 mM of crotonyl-CoA in the gel filtration buffer (100 mM NaCl, 20 mM Tris-HCl pH 7.9). Crystals appeared after several days in 2.0 M ...Details: Etr1p was crystallized at 15 mg/mL with 5 mM NADP and 5 mM of crotonyl-CoA in the gel filtration buffer (100 mM NaCl, 20 mM Tris-HCl pH 7.9). Crystals appeared after several days in 2.0 M (NH4)2SO4, 100 mM ADA/NaOH pH 6.4 at room temperature. The crystals were soaked in a solution containing 30% (v/v) glycerol, 2.0 M (NH4)2SO4, 100 mM ADA pH 6.4 prior to freezing in liquid nitrogen to prevent water-crystal formation. PH range: 6.2-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.73913 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.73913 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.04 Å / Num. obs: 41476 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rsym value: 0.044 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.511 / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4W99 Resolution: 2.5→46.749 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→46.749 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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