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- PDB-1yyt: D100E Trichodiene Synthase: Complex With Mg, Pyrophosphate, and (... -

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Basic information

Entry
Database: PDB / ID: 1yyt
TitleD100E Trichodiene Synthase: Complex With Mg, Pyrophosphate, and (4R)-7-azabisabolene
ComponentsTrichodiene synthase
KeywordsLYASE / terpenoid cyclase fold / site-directed mutant / Pyrophosphate / (4R)-7-azabisabolene
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
PYROPHOSPHATE 2- / Chem-SAZ / Trichodiene synthase
Similarity search - Component
Biological speciesFusarium sporotrichioides (fungus)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsVedula, L.S. / Rynkiewicz, M.J. / Pyun, H.J. / Coates, R.M. / Cane, D.E. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2005
Title: Molecular Recognition of the Substrate Diphosphate Group Governs Product Diversity in Trichodiene Synthase Mutants.
Authors: Vedula, L.S. / Rynkiewicz, M.J. / Pyun, H.J. / Coates, R.M. / Cane, D.E. / Christianson, D.W.
History
DepositionFeb 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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.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_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 23, 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)88,7717
Polymers88,1292
Non-polymers6415
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-72 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.703, 122.703, 151.297
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsAsymmetric unit is biological dimer

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Components

#1: Protein Trichodiene synthase / Sesquiterpene cyclase / TS


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, trichodiene synthase
#2: Chemical ChemComp-SAZ / (1S)-N,4-DIMETHYL-N-(4-METHYLPENT-3-ENYL)CYCLOHEX-3-ENAMINIUM / (4S)-7-AZABISABOLENE / S-AZABISABOLENE


Mass: 208.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H26N
#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-


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


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.67 Å3/Da / Density % sol: 66.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: PEG 8000, SODIUM HEPES, CALCIUM CHLORIDE , pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→14 Å / Num. obs: 31744 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 71 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 16.7
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2993 / % possible all: 93.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1KIZ

1kiz


Resolution: 2.9→14 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues with occupancy zero in entry were refined as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2010 6.8 %random
Rwork0.225 ---
all-29419 --
obs-26989 97.2 %-
Displacement parametersBiso mean: 51.1 Å2
Refinement stepCycle: LAST / Resolution: 2.9→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 41 71 5994
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_improper_angle_d0.8

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