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- PDB-3m00: Crystal Structure of 5-epi-aristolochene synthase M4 mutant compl... -

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Basic information

Entry
Database: PDB / ID: 3m00
TitleCrystal Structure of 5-epi-aristolochene synthase M4 mutant complexed with (2-cis,6-trans)-2-fluorofarnesyl diphosphate
ComponentsAristolochene synthase
KeywordsLYASE / plant terpenoid cyclase / 5-epi-aristolochene synthase / metal-binding domain / (2-cis / 6-trans)-2-fluorofarnesyl diphosphate / Magnesium / Metal-binding
Function / homology
Function and homology information


(+)-2-epi-prezizaene synthase / (-)-alpha-cedrene synthase / 5-epiaristolochene synthase / 5-epi-aristolochene synthase activity / sesquiterpene biosynthetic process / diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase ...Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Glycosyltransferase / Alpha/alpha barrel / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-2CF / 5-epi-aristolochene synthase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNoel, J.P. / Dellas, N. / Faraldos, J.A. / Zhao, M. / Hess Jr., B.A. / Smentek, L. / Coates, R.M. / O'Maille, P.E.
CitationJournal: Acs Chem.Biol. / Year: 2010
Title: Structural elucidation of cisoid and transoid cyclization pathways of a sesquiterpene synthase using 2-fluorofarnesyl diphosphates.
Authors: Noel, J.P. / Dellas, N. / Faraldos, J.A. / Zhao, M. / Hess, B.A. / Smentek, L. / Coates, R.M. / O'Maille, P.E.
History
DepositionMar 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6835
Polymers63,2101
Non-polymers4734
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.100, 126.100, 122.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Aristolochene synthase / 5-epi-aristolochene synthase / EAS


Mass: 63209.758 Da / Num. of mol.: 1 / Mutation: A274T, V372I, Y406L, V516I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: EAS3, EAS4 / Plasmid: pHis9GW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q40577, aristolochene synthase
#2: Chemical ChemComp-2CF / (2E,6E)-2-fluoro-3,7,11-trimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate


Mass: 400.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H27FO7P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 3.85 Å3/Da / Density % sol: 68.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG 8000, 200 mM magnesium acetate, 100 mM MOPSO, pH 7.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2005
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 62326 / Num. obs: 61361 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.01 % / Biso Wilson estimate: 38.567 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.76
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 3.6 / Num. measured obs: 30095 / Num. unique all: 8174 / Num. unique obs: 7714 / % possible all: 94.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5EAT

5eat


Resolution: 2.1→43.91 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.259 2885 5 %
Rwork0.221 --
obs-57483 99 %
Solvent computationBsol: 47.306 Å2
Displacement parametersBiso max: 97.32 Å2 / Biso mean: 44.636 Å2 / Biso min: 20.02 Å2
Baniso -1Baniso -2Baniso -3
1--13.068 Å20 Å20 Å2
2---13.068 Å20 Å2
3---26.135 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 28 372 4702
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4141.5
X-RAY DIFFRACTIONc_scbond_it2.1832
X-RAY DIFFRACTIONc_mcangle_it2.3032
X-RAY DIFFRACTIONc_scangle_it3.2942.5
LS refinement shellHighest resolution: 2.1 Å
RfactorNum. reflection
Rfree0.2586 2885
Rwork0.2205 -
obs-57483
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3C2F_par.txt
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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