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- PDB-5l4s: Isopiperitenone reductase from Mentha piperita in complex with NA... -

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Basic information

Entry
Database: PDB / ID: 5l4s
TitleIsopiperitenone reductase from Mentha piperita in complex with NADP and beta-Cyclocitral
Components(-)-isopiperitenone reductase
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase/reductases (SDR) / Rossmann fold / beta-cyclocitral / isopiperitenone
Function / homology
Function and homology information


(-)-isopiperitenone reductase / menthol biosynthetic process / (-)-isopiperitenone reductase activity / terpene metabolic process / NADPH binding / membrane / cytoplasm
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-cyclocitral / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / (-)-isopiperitenone reductase
Similarity search - Component
Biological speciesMentha piperita (peppermint)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsKaruppiah, V. / Toogood, H.S. / Leys, D. / Scrutton, N.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J015512/1 and BB/M000354/1 United Kingdom
CitationJournal: 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
DepositionMay 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (-)-isopiperitenone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7183
Polymers34,8221
Non-polymers8962
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-4 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.113, 65.612, 94.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein (-)-isopiperitenone reductase


Mass: 34822.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mentha piperita (peppermint) / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WAU1, (-)-isopiperitenone reductase
#2: Chemical ChemComp-6KX / beta-cyclocitral


Mass: 152.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.09 M NPS (0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3M Ammonium sulfate), 0.1 M Buffer sytem 1 pH 6.5 (1M Imidazole; MES monohydrate), 50% Precipitant mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.41→53.95 Å / Num. obs: 72941 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.4
Reflection shellResolution: 1.41→1.45 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(dev_2294: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O26

3o26


Resolution: 1.41→50.769 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.44
RfactorNum. reflection% reflection
Rfree0.1831 3587 4.94 %
Rwork0.1532 --
obs0.1547 72557 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.6 Å2
Refinement stepCycle: LAST / Resolution: 1.41→50.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 59 300 2756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162518
X-RAY DIFFRACTIONf_angle_d1.4923422
X-RAY DIFFRACTIONf_dihedral_angle_d16.202932
X-RAY DIFFRACTIONf_chiral_restr0.096385
X-RAY DIFFRACTIONf_plane_restr0.009434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.42860.35731260.33112571X-RAY DIFFRACTION97
1.4286-1.44810.33111440.32122561X-RAY DIFFRACTION99
1.4481-1.46880.31811350.29372600X-RAY DIFFRACTION98
1.4688-1.49070.33421340.2792620X-RAY DIFFRACTION99
1.4907-1.5140.32531140.25712637X-RAY DIFFRACTION99
1.514-1.53890.28351500.23372630X-RAY DIFFRACTION99
1.5389-1.56540.23961320.22232605X-RAY DIFFRACTION99
1.5654-1.59390.30171370.20982609X-RAY DIFFRACTION99
1.5939-1.62450.21511320.19492660X-RAY DIFFRACTION100
1.6245-1.65770.1971350.1852593X-RAY DIFFRACTION99
1.6577-1.69370.24341400.17152627X-RAY DIFFRACTION99
1.6937-1.73310.1941390.16272642X-RAY DIFFRACTION100
1.7331-1.77650.19731510.15322643X-RAY DIFFRACTION100
1.7765-1.82450.19021530.14852622X-RAY DIFFRACTION100
1.8245-1.87820.18341310.14582642X-RAY DIFFRACTION100
1.8782-1.93880.19591470.13222673X-RAY DIFFRACTION100
1.9388-2.00810.15141260.12512638X-RAY DIFFRACTION100
2.0081-2.08850.1761310.12122638X-RAY DIFFRACTION100
2.0885-2.18360.14071420.11992683X-RAY DIFFRACTION100
2.1836-2.29870.13551360.11772654X-RAY DIFFRACTION100
2.2987-2.44270.14631470.11722686X-RAY DIFFRACTION100
2.4427-2.63130.17731420.12822687X-RAY DIFFRACTION100
2.6313-2.89610.17131310.13422706X-RAY DIFFRACTION100
2.8961-3.31510.18281310.14822733X-RAY DIFFRACTION100
3.3151-4.17640.14671410.14232746X-RAY DIFFRACTION100
4.1764-50.80180.1651600.14922864X-RAY DIFFRACTION100

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