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- PDB-7eql: Crystal structure of (+)-pulegone reductase from Mentha piperita -

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Basic information

Entry
Database: PDB / ID: 7eql
TitleCrystal structure of (+)-pulegone reductase from Mentha piperita
Components(+)-pulegone reductase
KeywordsPLANT 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
Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / N-terminal domain of oxidoreductase / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
(+)-pulegone reductase
Similarity search - Component
Biological speciesMentha piperita (peppermint)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsLin, W.
CitationJournal: 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
DepositionMay 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (+)-pulegone reductase


Theoretical massNumber of molelcules
Total (without water)37,9531
Polymers37,9531
Non-polymers00
Water00
1
A: (+)-pulegone reductase

A: (+)-pulegone reductase


Theoretical massNumber of molelcules
Total (without water)75,9052
Polymers75,9052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area2790 Å2
ΔGint-24 kcal/mol
Surface area28190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.111, 120.111, 57.626
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein (+)-pulegone reductase


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

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.1 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.72-2.874.20.473789818620.8730.2550.5393.199.3
8.6-104.023.30.02913434040.9980.0180.03431.792.3

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hfj

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
RfactorNum. reflection% reflection
Rfree0.3021 695 5.59 %
Rwork0.2751 11727 -
obs0.2767 12422 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.61 Å2 / Biso mean: 112.1952 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.72→104.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2623 0 0 0 2623
Num. residues----338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.72-2.92970.40291390.3957241299
2.9297-3.22450.41881610.3824235999
3.2245-3.69110.43281450.3558223892
3.6911-4.65050.26041150.2604233095
4.6505-500.26931350.2336238895

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