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Yorodumi- PDB-5ldg: Isopiperitenone reductase from Mentha piperita in complex with Is... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ldg | ||||||
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Title | Isopiperitenone reductase from Mentha piperita in complex with Isopiperitenone and NADP | ||||||
Components | (-)-isopiperitenone reductase(-)-Isopiperitenone reductase | ||||||
Keywords | OXIDOREDUCTASE / short-chain dehydrogenases/reductases (SDR) / Rossmann fold / Isopiperitenone / Isopulegone | ||||||
Function / homology | Function and homology information (-)-isopiperitenone reductase / menthol biosynthetic process / (-)-isopiperitenone reductase activity / terpene metabolic process / NADPH binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mentha piperita (peppermint) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Karuppiah, V. / Toogood, H.S. / Leys, D. / Scrutton, N.S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2016 Title: Pinpointing a Mechanistic Switch Between Ketoreduction and "Ene" Reduction in Short-Chain Dehydrogenases/Reductases. Authors: Lygidakis, A. / Karuppiah, V. / Hoeven, R. / Ni Cheallaigh, A. / Leys, D. / Gardiner, J.M. / Toogood, H.S. / Scrutton, N.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ldg.cif.gz | 211.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ldg.ent.gz | 171.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ldg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/5ldg ftp://data.pdbj.org/pub/pdb/validation_reports/ld/5ldg | HTTPS FTP |
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-Related structure data
Related structure data | 5l4sC 5l51C 5l53C 5lcxC 3o26S 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: 34579.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mentha piperita (peppermint) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WAU1, (-)-isopiperitenone reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-IT9 / (-)- |
#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: 2.73 Å3/Da / Density % sol: 54.9 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.06M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate), 0.1M Buffer system 3 pH 8.5 (1M Tris (base); BICINE), 50% Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→60.56 Å / Num. obs: 92810 / % possible obs: 99.2 % / Redundancy: 6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 5.1 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O26 Resolution: 1.3→53.939 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 11.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→53.939 Å
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Refine LS restraints |
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LS refinement shell |
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