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- PDB-2q9y: Trichodiene synthase: Complex with Mg, inorganic pyrophosphate, a... -

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Basic information

Entry
Database: PDB / ID: 2q9y
TitleTrichodiene synthase: Complex with Mg, inorganic pyrophosphate, and benzyl triethyl ammonium cation
ComponentsTrichodiene synthase
KeywordsLYASE / terpenoid synthase fold / benzyl triethyl ammonium chloride / inorganic pyrophosphate
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
N-benzyl-N,N-diethylethanaminium / PYROPHOSPHATE 2- / Trichodiene synthase
Similarity search - Component
Biological speciesFusarium sporotrichioides (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.85 Å
AuthorsVedula, L.S. / Zhao, Y. / Coates, R.M. / Koyama, T. / Cane, D.E. / Christianson, D.W.
CitationJournal: Arch.Biochem.Biophys. / Year: 2007
Title: Exploring biosynthetic diversity with trichodiene synthase.
Authors: Vedula, L.S. / Zhao, Y. / Coates, R.M. / Koyama, T. / Cane, D.E. / Christianson, D.W.
History
DepositionJun 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / 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.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_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)88,6679
Polymers88,1012
Non-polymers5657
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-61.5 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.488, 122.488, 150.494
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Trichodiene synthase / Sesquiterpene cyclase / TS


Mass: 44050.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium sporotrichioides (fungus) / Gene: TRI5, TOX 5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13513, trichodiene synthase

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Non-polymers , 5 types, 33 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#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-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-BTM / N-benzyl-N,N-diethylethanaminium


Mass: 192.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 66.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: HEPES, PEG 8000, Calcium chloride, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 29316 / Num. obs: 27213 / % possible obs: 94.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 2.6
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2957

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1JFG

1jfg


Resolution: 2.85→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: All side chains with occupancies = 0 were refined as alanines and modeled in the best possible conformation, post-refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1306 -random
Rwork0.216 ---
all-30999 --
obs-27092 87.4 %-
Displacement parametersBiso mean: 64.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5846 0 34 26 5906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d0.8

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