+Open data
-Basic information
Entry | Database: PDB / ID: 7eql | ||||||
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Title | Crystal structure of (+)-pulegone reductase from Mentha piperita | ||||||
Components | (+)-pulegone reductase | ||||||
Keywords | PLANT PROTEIN / double bond reductase | ||||||
Function / homology | Function and homology information (+)-pulegone reductase / (+)-pulegone reductase (NADP+) activity / : / terpene metabolic process / terpenoid biosynthetic process / NADPH binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mentha piperita (peppermint) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | ||||||
Authors | Lin, W. | ||||||
Citation | Journal: Front Plant Sci / Year: 2021 Title: Functional Characterization and Structural Insights Into Stereoselectivity of Pulegone Reductase in Menthol Biosynthesis. Authors: Liu, C. / Gao, Q. / Shang, Z. / Liu, J. / Zhou, S. / Dang, J. / Liu, L. / Lange, I. / Srividya, N. / Lange, B.M. / Wu, Q. / Lin, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eql.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eql.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 7eql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eql_validation.pdf.gz | 429.3 KB | Display | wwPDB validaton report |
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Full document | 7eql_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 7eql_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 7eql_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/7eql ftp://data.pdbj.org/pub/pdb/validation_reports/eq/7eql | HTTPS FTP |
-Related structure data
Related structure data | 4hfjS 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: 37952.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mentha piperita (peppermint) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q6WAU0, (+)-pulegone reductase |
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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: 3.16 Å3/Da / Density % sol: 61.1 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1M Ammonium sulfate , 0.1 M Bis-Tris (pH 5.5), 1% W/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.72→104.02 Å / Num. obs: 12444 / % possible obs: 96.3 % / Redundancy: 4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.019 / Rrim(I) all: 0.039 / Net I/σ(I): 19.6 / Num. measured all: 50025 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4hfj Resolution: 2.72→104.019 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 37.73 / 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: 170.61 Å2 / Biso mean: 112.1952 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.72→104.019 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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