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- PDB-3c1o: The multiple phenylpropene synthases in both Clarkia breweri and ... -

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Basic information

Entry
Database: PDB / ID: 3c1o
TitleThe multiple phenylpropene synthases in both Clarkia breweri and Petunia hybrida represent two distinct lineages
Componentseugenol synthase
KeywordsOXIDOREDUCTASE / eugenol / phenylpropene / PIP reductase / short-chain dehydrogenase/reductase
Function / homology
Function and homology information


eugenol synthase / phenylpropanoid biosynthetic process / oxidoreductase activity / nucleotide binding
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Eugenol synthase 1
Similarity search - Component
Biological speciesClarkia breweri (fairy fans)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLouie, G.V. / Noel, J.P. / Bowman, M.E.
CitationJournal: Plant J. / Year: 2008
Title: The multiple phenylpropene synthases in both Clarkia breweri and Petunia hybrida represent two distinct protein lineages.
Authors: Koeduka, T. / Louie, G.V. / Orlova, I. / Kish, C.M. / Ibdah, M. / Wilkerson, C.G. / Bowman, M.E. / Baiga, T.J. / Noel, J.P. / Dudareva, N. / Pichersky, E.
History
DepositionJan 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: eugenol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0852
Polymers36,3421
Non-polymers7431
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: eugenol synthase
hetero molecules

A: eugenol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1714
Polymers72,6842
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area4650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.330, 87.381, 51.545
Angle α, β, γ (deg.)90.000, 101.330, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1201-

HOH

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Components

#1: Protein eugenol synthase / Brewer's clarkia


Mass: 36341.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clarkia breweri (fairy fans) / Gene: EGS1 / Plasmid: pHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D0VWT0*PLUS
#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.: 210 / 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: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1 M sodium citrate, 20% (w/v) PEG 4000, 20% (v/v) isopropanol, 2 mM dithiothreitol, 5 mM NADP+, pH 5.4, 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: Nov 2, 2007
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.434→50.572 Å / Num. obs: 26859 / % possible obs: 99 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.93.50.4011.81300037020.40193.2
1.9-2.013.90.2632.71437837020.263100
2.01-2.153.90.1754.11380735340.175100
2.15-2.323.90.1344.91267532640.134100
2.32-2.553.90.1076.31173430070.107100
2.55-2.853.90.0837.91057927320.083100
2.85-3.293.90.0718.7926924060.071100
3.29-4.023.80.05910.1767520370.05999.9
4.02-5.693.60.05211.1572615870.05299.9
5.69-50.5740.03415.735338880.03499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.482 / Cor.coef. Fo:Fc: 0.412
Highest resolutionLowest resolution
Rotation3 Å33.91 Å
Translation3 Å33.91 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.9 Å / FOM work R set: 0.879 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1347 5 %random
Rwork0.186 ---
obs-26856 99 %-
Solvent computationBsol: 45.886 Å2
Displacement parametersBiso mean: 21.385 Å2
Baniso -1Baniso -2Baniso -3
1--2.651 Å20 Å2-0.04 Å2
2---0.563 Å20 Å2
3---3.213 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 48 210 2758
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.7862
X-RAY DIFFRACTIONc_scbond_it2.9382.5
X-RAY DIFFRACTIONc_mcangle_it2.653
X-RAY DIFFRACTIONc_scangle_it4.4344
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_deg1.33
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2ndp.par
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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