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- PDB-1jfa: Trichodiene Synthase from Fusarium Sporotrichioides -

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Basic information

Entry
Database: PDB / ID: 1jfa
TitleTrichodiene Synthase from Fusarium Sporotrichioides
ComponentsTRICHODIENE SYNTHASE
KeywordsLYASE / terpenoid synthase fold
Function / homology
Function and homology information


trichodiene synthase / trichodiene synthase activity / sesquiterpenoid biosynthetic process / metal ion binding
Similarity search - Function
Trichodiene synthase, ascomycetes / Trichodiene synthase / Trichodiene synthase (TRI5) / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Trichodiene synthase
Similarity search - Component
Biological speciesFusarium sporotrichioides (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Single isomorphous replacement with anomalous scattering / Resolution: 2.5 Å
AuthorsRynkiewicz, M.J. / Cane, D.E. / Christianson, D.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structure of trichodiene synthase from Fusarium sporotrichioides provides mechanistic inferences on the terpene cyclization cascade.
Authors: Rynkiewicz, M.J. / Cane, D.E. / Christianson, D.W.
History
DepositionJun 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2001Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 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

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Assembly

Deposited unit
A: TRICHODIENE SYNTHASE
B: TRICHODIENE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3496
Polymers88,1012
Non-polymers2484
Water4,810267
1
A: TRICHODIENE SYNTHASE
hetero molecules

B: TRICHODIENE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3496
Polymers88,1012
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-x+y,-z+1/31
Buried area6280 Å2
ΔGint-28 kcal/mol
Surface area27640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.164, 122.164, 151.247
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

#1: Protein TRICHODIENE SYNTHASE / E.C.4.1.99.6 / SESQUITERPENE CYCLASE / TS / TRICHODIENE SYNTHASE TRI5


Mass: 44050.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium sporotrichioides (fungus) / Gene: TRI5 / Plasmid: PZW03 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13513, EC: 4.1.99.6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 3.7 Å3/Da / Density % sol: 66.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: PEG 4000, calcium chloride, sodium HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP at 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlenzyme1drop
20.1 MHEPES1reservoirpH6.9
350 mM1reservoirCaCl2
46-10 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: SBC-2 / Detector: CCD / Date: Feb 25, 2001
RadiationMonochromator: Si-111 + Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 45629 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 9.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.285 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 99.1 % / Num. measured all: 386732 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 94.5 % / Rmerge(I) obs: 0.31

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Processing

Software
NameClassification
DMmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: Single isomorphous replacement with anomalous scattering
Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2505 3196 random
Rwork0.2181 --
all-40676 -
obs-40676 -
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5844 0 16 267 6127
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_bond_d0.0074
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.3291 355 -
Rwork0.2765 --
obs-3130 77 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Num. reflection obs: 37480 / σ(F): 0 / Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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