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- PDB-27ho: The structure of cis-isoeugenol synthase -

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Basic information

Entry
Database: PDB / ID: 27ho
TitleThe structure of cis-isoeugenol synthase
ComponentsIsoeugenol synthase 1
KeywordsPLANT PROTEIN / cis-isoeugenol synthase / Short-chain dehydrogenases/reductases
Function / homologyChem-NDP
Function and homology information
Biological speciesAcorus tatarinowii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.60096709433 Å
AuthorsLong, G.F. / Wang, G.Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis for cis-phenylpropene biosynthesis by dual conformational selection of substrate and reaction intermediate
Authors: Long, G.F. / Wang, G.Q.
History
DepositionJun 1, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoeugenol synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2122
Polymers36,4671
Non-polymers7451
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-3 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.340, 139.340, 139.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Isoeugenol synthase 1


Mass: 36467.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acorus tatarinowii (plant) / Production host: Rosetta (plant)
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 289.2 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12.5% PEG 1000, PEG 3350, 12.5% MPD, 0.03 M of each halide, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→56.89 Å / Num. obs: 14022 / % possible obs: 100 % / Redundancy: 9.3 % / CC1/2: 0.999 / Net I/σ(I): 18.3
Reflection shellResolution: 2.6→2.72 Å / Num. unique obs: 1698 / CC1/2: 0.701 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.60096709433→34.835 Å / SU ML: 0.364130368105 / Cross valid method: FREE R-VALUE / σ(F): 1.3647199372 / Phase error: 29.3540959833
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.283710314343 697 4.97892706622 %
Rwork0.23553300769 13302 -
obs0.237800858707 13999 99.9286173174 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.8518495585 Å2
Refinement stepCycle: LAST / Resolution: 2.60096709433→34.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 48 16 2393
Refine LS restraintsType: f_bond_d / Dev ideal: 0.00311777514492 / Number: 2417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.601-2.80170.3432738131341480.2865631471932648X-RAY DIFFRACTION99.9642474079
2.8017-3.08350.3636693802191480.2781486715552594X-RAY DIFFRACTION100
3.0835-3.52930.3340467375781380.2589528444342650X-RAY DIFFRACTION100
3.5293-4.44510.2629124522281340.2136493194362669X-RAY DIFFRACTION100

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