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Yorodumi- PDB-6ghw: Substituting the prolines of 4-oxalocrotonate tautomerase with no... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ghw | ||||||
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Title | Substituting the prolines of 4-oxalocrotonate tautomerase with non-canonical analogue (2S)-3,4-dehydroproline | ||||||
Components | 2-hydroxymuconate tautomerase | ||||||
Keywords | ISOMERASE / non-canonical amino acid / (2S)-3 / 4-dehydroproline | ||||||
Function / homology | Function and homology information xylene catabolic process / 2-hydroxymuconate tautomerase / toluene catabolic process / isomerase activity Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Pavkov-Keller, T. / Lukesch, M.S. / Wiltschi, B. / Gruber, K. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Sci Rep / Year: 2019 Title: Substituting the catalytic proline of 4-oxalocrotonate tautomerase with non-canonical analogues reveals a finely tuned catalytic system. Authors: Lukesch, M.S. / Pavkov-Keller, T. / Gruber, K. / Zangger, K. / Wiltschi, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ghw.cif.gz | 47.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ghw.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ghw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/6ghw ftp://data.pdbj.org/pub/pdb/validation_reports/gh/6ghw | HTTPS FTP |
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-Related structure data
Related structure data | 4x19S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 6817.809 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xylH / Production host: Escherichia coli (E. coli) / References: UniProt: Q01468, 2-hydroxymuconate tautomerase #2: Chemical | ChemComp-CA / | #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: 2.67 Å3/Da / Density % sol: 53.91 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 88% of 1-45 Morpheus condition (0.12M Alcohols, 0.1M Tris (base), BICINE pH 8.5, 50% v/v Precipitant mix composed of 40% v/v PEG 500 MME; 20 % w/v PEG 20000). protein concentration 6 mg/ml n ...Details: 88% of 1-45 Morpheus condition (0.12M Alcohols, 0.1M Tris (base), BICINE pH 8.5, 50% v/v Precipitant mix composed of 40% v/v PEG 500 MME; 20 % w/v PEG 20000). protein concentration 6 mg/ml n 0.1M PCTP buffer pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Feb 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35.98 Å / Num. obs: 9550 / % possible obs: 96 % / Redundancy: 2.8 % / Biso Wilson estimate: 27.37 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.114 / Rrim(I) all: 0.199 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.541 / Num. unique obs: 764 / CC1/2: 0.62 / Rpim(I) all: 0.405 / Rrim(I) all: 0.68 / % possible all: 78.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4x19 Resolution: 2.3→35.934 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36 Details: Only 3 molecules could be build in the electron density. The fourth molecule can be seen but the density is interupted and not clearly defined (probably several conformations of this ...Details: Only 3 molecules could be build in the electron density. The fourth molecule can be seen but the density is interupted and not clearly defined (probably several conformations of this molecule - that with symmetry forms one of the hexamers). Therefore, we omitted the molecule 4 from the refinement. This also has a direct relation on higher Rfactors.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→35.934 Å
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Refine LS restraints |
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LS refinement shell |
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