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- PDB-5l53: Menthone neomenthol reductase from Mentha piperita in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5l53
TitleMenthone neomenthol reductase from Mentha piperita in complex with NADP
Components(-)-menthone:(+)-neomenthol reductase
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase/reductases (SDR) / Rossmann fold / Menthone / Isomenthone
Function / homology
Function and homology information


(+)-neomenthol dehydrogenase activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / nucleotide binding / membrane
Similarity search - Function
Carbonyl reductase [NADPH] 1-like / short chain dehydrogenase / Enoyl-(Acyl carrier protein) reductase / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Short-chain dehydrogenase/reductase
Similarity search - Component
Biological speciesMentha piperita (peppermint)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 27, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (-)-menthone:(+)-neomenthol reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2942
Polymers35,5511
Non-polymers7431
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-2 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.125, 80.125, 255.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein (-)-menthone:(+)-neomenthol reductase


Mass: 35551.012 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: Q06ZW2, EC: 1.1.1.208
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M imidazole pH 8 and 1M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.24→63.793 Å / Num. obs: 20604 / % possible obs: 100 % / Redundancy: 25.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.128 / Net I/σ(I): 15
Reflection shellResolution: 2.24→2.3 Å / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2386: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O26

3o26


Resolution: 2.24→63.793 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.47
RfactorNum. reflection% reflection
Rfree0.2578 1031 5.04 %
Rwork0.2078 --
obs0.2104 20444 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.24→63.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 48 33 2355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122370
X-RAY DIFFRACTIONf_angle_d1.1323214
X-RAY DIFFRACTIONf_dihedral_angle_d12.021442
X-RAY DIFFRACTIONf_chiral_restr0.059359
X-RAY DIFFRACTIONf_plane_restr0.007431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.35810.44841440.35972707X-RAY DIFFRACTION99
2.3581-2.50590.40711360.32472694X-RAY DIFFRACTION99
2.5059-2.69930.30441480.282712X-RAY DIFFRACTION99
2.6993-2.9710.35041610.2532737X-RAY DIFFRACTION99
2.971-3.40090.36441520.23032757X-RAY DIFFRACTION100
3.4009-4.28460.20011310.17752830X-RAY DIFFRACTION100
4.2846-63.81910.18841590.16422976X-RAY DIFFRACTION100

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