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- PDB-2r2g: Structure of Eugenol Synthase from Ocimum basilicum complexed wit... -

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Basic information

Entry
Database: PDB / ID: 2r2g
TitleStructure of Eugenol Synthase from Ocimum basilicum complexed with EMDF
ComponentsEugenol synthase 1
KeywordsPLANT PROTEIN / eugenol / phenylpropene / PIP reductase / short-chain dehydrogenase/reductase
Function / homology
Function and homology information


eugenol biosynthetic process / eugenol synthase / oxidoreductase activity / nucleotide binding / protein homodimerization activity
Similarity search - Function
Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold ...Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EMF / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Eugenol synthase 1
Similarity search - Component
Biological speciesOcimum basilicum (sweet basil)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLouie, G.V. / Noel, J.P. / Bowman, M.E.
CitationJournal: Plos One / Year: 2007
Title: Structure and reaction mechanism of basil eugenol synthase
Authors: Louie, G.V. / Baiga, T.J. / Bowman, M.E. / Koeduka, T. / Taylor, J.H. / Spassova, S.M. / Pichersky, E. / Noel, J.P.
History
DepositionAug 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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: Eugenol synthase 1
B: Eugenol synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9366
Polymers71,9772
Non-polymers1,9594
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.763, 86.197, 76.933
Angle α, β, γ (deg.)90.00, 107.40, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a monomer (half of the asymmetric unit)

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Components

#1: Protein Eugenol synthase 1


Mass: 35988.414 Da / Num. of mol.: 2 / Mutation: K132Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ocimum basilicum (sweet basil) / Gene: EGS1 / Plasmid: pHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15GI4
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-EMF / ethyl (1S,2S)-2-(4-hydroxy-3-methoxyphenyl)cyclopropanecarboxylate


Mass: 236.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium succinate, 21% PEG 3350, 0.3 M KCl, 2 mM dithiothreitol, 5 mM NADP+, pH 5.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2006
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→44.151 Å / Num. obs: 57391 / % possible obs: 92.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 4.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.92.20.3412.11621774840.34182.6
1.9-2.012.20.242.21545570210.2482.2
2.01-2.152.40.1973.51707070180.19787.1
2.15-2.322.80.1812.62025573030.18197.4
2.32-2.5530.1454.52024867770.14597.8
2.55-2.853.90.1344.72418462090.13499.4
2.85-3.293.80.1055.82080655020.10599.2
3.29-4.023.40.0896.41566446060.08998.1
4.02-5.693.20.086.81110535060.0896.4
5.69-44.153.50.0657.7693819650.06596.4

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNS1.1refinement
PDB_EXTRACT3data extraction
BOSdata collection
MOSFLMdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QYC

1qyc


Resolution: 1.8→44.09 Å / FOM work R set: 0.816 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.28 2918 4.7 %
Rwork0.248 --
obs-57422 92.6 %
Solvent computationBsol: 47.148 Å2
Displacement parametersBiso mean: 22.304 Å2
Baniso -1Baniso -2Baniso -3
1--2.984 Å20 Å25.853 Å2
2--0.399 Å20 Å2
3---2.585 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4954 0 130 350 5434
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.8432
X-RAY DIFFRACTIONc_scbond_it2.8292.5
X-RAY DIFFRACTIONc_mcangle_it2.5753
X-RAY DIFFRACTIONc_scangle_it4.1054
X-RAY DIFFRACTIONc_bond_d0.0063
X-RAY DIFFRACTIONc_angle_deg1.28
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ndp.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4EMF.par

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