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Yorodumi- PDB-7djs: Crystal structure of isopiperitenol dehydrogenase from Pseudomona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7djs | ||||||
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Title | Crystal structure of isopiperitenol dehydrogenase from Pseudomonas aeruginosa complexed with NAD | ||||||
Components | SDR family oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / complex / NAD | ||||||
Function / homology | Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SDR family oxidoreductase Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Zhan, J.R. / Zheng, Y.C. | ||||||
Citation | Journal: Adv.Synth.Catal. / Year: 2021 Title: Discovery and Engineering of Bacterial (-)-Isopiperitenol Dehydrogenases to Enhance (-)-Menthol Precursor Biosynthesis. Authors: Zhan, J.R. / Shou, C. / Zheng, Y.C. / Chen, Q. / Pan, J. / Li, C.X. / Xu, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7djs.cif.gz | 206.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7djs.ent.gz | 163 KB | Display | PDB format |
PDBx/mmJSON format | 7djs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/7djs ftp://data.pdbj.org/pub/pdb/validation_reports/dj/7djs | HTTPS FTP |
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-Related structure data
Related structure data | 5x8hS 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: 26812.752 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: DY930_09865, F7O90_18305, FDK04_18370, IPC116_19850, IPC36_02985 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A554HE32 #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.25 Details: 100mM MES-imidazole pH 6.25, 30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 20% v/v PEG 500MME, 10% w/v PEG 20000 PH range: 6.25-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 100875 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.992 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.7→1.73 Å / Num. unique obs: 5009 / CC1/2: 0.952 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X8H Resolution: 1.7→42.23 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.54 Å2 / Biso mean: 16.0461 Å2 / Biso min: 2.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→42.23 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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