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- PDB-1kiz: D100E trichodiene synthase complexed with pyrophosphate -

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Basic information

Entry
Database: PDB / ID: 1kiz
TitleD100E trichodiene synthase complexed with pyrophosphate
Componentstrichodiene synthase
KeywordsLYASE / terpenoid synthase fold / site-directed mutant / pyrophosphate
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: 2.6 Å
AuthorsRynkiewicz, M.J. / Cane, D.E. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2002
Title: X-ray crystal structures of D100E trichodiene synthase and its pyrophosphate complex reveal the basis for terpene product diversity.
Authors: Rynkiewicz, M.J. / Cane, D.E. / Christianson, D.W.
History
DepositionDec 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_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_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 16, 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: trichodiene synthase
B: trichodiene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6029
Polymers88,1292
Non-polymers4737
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-49 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.723, 122.723, 151.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsTo generate the biological dimer from the asymmetric unit, apply tranformation 6_665 to chain A and 6_655 to chain B

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Components

#1: Protein trichodiene synthase /


Mass: 44064.629 Da / Num. of mol.: 2 / Mutation: D100E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium sporotrichioides (fungus) / Gene: Tri5 / 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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.: 226 / 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: 3.72 Å3/Da / Density % sol: 66.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: PEG 8000, calcium chloride, sodium HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Details: Rynkiewicz, M.J., (2001) Proc.Natl.Acad.Sci.U.S.J., 98, 13543.
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 14, 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: 2.6→25 Å / Num. all: 41296 / Num. obs: 41214 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 42.2 Å2
Reflection shellResolution: 2.59→2.69 Å / Redundancy: 6.2 % / % possible all: 100
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 246608 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.237

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Processing

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

1jfg


Resolution: 2.6→24.49 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2061956.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3111 7.6 %RANDOM
Rwork0.219 ---
obs-40791 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.3452 Å2 / ksol: 0.324764 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å25.73 Å20 Å2
2--1.51 Å20 Å2
3----3.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.6→24.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 27 226 6135
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 572 8.5 %
Rwork0.282 6137 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMPOP.TOP
X-RAY DIFFRACTION3EDO.PARAMWATER.TOP
X-RAY DIFFRACTION4POP.PARION.TOP
X-RAY DIFFRACTION5ION.PARAMEDO.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 7.6 % / Rfactor obs: 0.223 / Rfactor Rfree: 0.256
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.334 / % reflection Rfree: 8.5 % / Rfactor Rwork: 0.282

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