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- PDB-1jfg: TRICHODIENE SYNTHASE FROM FUSARIUM SPOROTRICHIOIDES COMPLEXED WIT... -

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Basic information

Entry
Database: PDB / ID: 1jfg
TitleTRICHODIENE SYNTHASE FROM FUSARIUM SPOROTRICHIOIDES COMPLEXED WITH DIPHOSPHATE
ComponentsTRICHODIENE SYNTHASE
KeywordsLYASE / terpenoid synthase fold
Function / homology
Function and homology information


trichodiene synthase / sesquiterpenoid biosynthetic process / trichodiene synthase activity / 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
PYROPHOSPHATE 2- / Trichodiene synthase
Similarity search - Component
Biological speciesFusarium sporotrichioides (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / 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 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: TRICHODIENE SYNTHASE
B: TRICHODIENE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6269
Polymers88,1012
Non-polymers5257
Water5,260292
1
A: TRICHODIENE SYNTHASE
hetero molecules

B: TRICHODIENE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6269
Polymers88,1012
Non-polymers5257
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-x+y,-z+1/31
2
B: TRICHODIENE SYNTHASE
hetero molecules

A: TRICHODIENE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6269
Polymers88,1012
Non-polymers5257
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+1/31
Buried area7020 Å2
ΔGint-71 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.574, 122.574, 150.869
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.71 Å3/Da / Density % sol: 66.87 %
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: NSLS / Beamline: X12C / Wavelength: 1.01 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 3, 2000
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 46785 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.5
Reflection shellResolution: 2.48→2.58 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.306 / % possible all: 99.6

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1JFA

1jfa


Resolution: 2.5→14.9 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3333 7.9 %RANDOM
Rwork0.217 ---
all-42182 --
obs-42182 --
Displacement parametersBiso mean: 34.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5880 0 30 292 6202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.335 627 -
Rwork0.289 --
obs-5726 84.5 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Num. reflection obs: 38849 / σ(F): 0 / % reflection Rfree: 7.9 % / Rfactor obs: 0.22 / Rfactor Rfree: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shell
*PLUS
Rfactor Rfree: 0.335 / Rfactor Rwork: 0.289

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