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- PDB-5eau: 5-EPI-ARISTOLOCHENE SYNTHASE FROM NICOTIANA TABACUM -

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Basic information

Entry
Database: PDB / ID: 5eau
Title5-EPI-ARISTOLOCHENE SYNTHASE FROM NICOTIANA TABACUM
Components5-EPI-ARISTOLOCHENE SYNTHASE
KeywordsISOPRENOID SYNTHASE / 5-EPI-ARISTOLOCHENE SYNTHASE / NATURAL PRODUCTS BIOSYNTHESIS / ISOPRENOID CYCLASE
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
TRIFLUOROFURNESYL DIPHOSPHATE / 5-epi-aristolochene synthase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.15 Å
AuthorsStarks, C.M. / Back, K. / Chappell, J. / Noel, J.P.
Citation
Journal: Science / Year: 1997
Title: Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase.
Authors: Starks, C.M. / Back, K. / Chappell, J. / Noel, J.P.
#1: Journal: Arch.Biochem.Biophys. / Year: 1994
Title: Expression of a Plant Sesquiterpene Cyclase Gene in Escherichia Coli
Authors: Back, K. / Yin, S. / Chappell, J.
#2: Journal: Plant Physiol. / Year: 1993
Title: Purification and Characterization of an Inducible Sesquiterpene Cyclase from Elicitor-Treated Tobacco Cell Suspension Cultures
Authors: Vogeli, U. / Freeman, J.W. / Chappell, J.
History
DepositionDec 11, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-EPI-ARISTOLOCHENE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5284
Polymers63,0431
Non-polymers4853
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.960, 125.960, 122.970
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 5-EPI-ARISTOLOCHENE SYNTHASE / 5-EPI-ARISTOLOCHENE CYCLASE


Mass: 63043.484 Da / Num. of mol.: 1 / Mutation: EXPRESSED WITH 6-HIS TAG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Strain: BL21 (DE3) / Cell line: BL21 / Cellular location: CYTOPLASM / Plasmid: PET28B(+) / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q40577
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FFF / TRIFLUOROFURNESYL DIPHOSPHATE


Mass: 436.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25F3O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.87 Å3/Da / Density % sol: 68 %
Crystal growpH: 6.9
Details: PROTEIN WAS CRYSTALLIZED FROM 15% PEG 8000, 200 MM MG(OAC)2, 100 MM MOPSO PH 6.9, 1MM DTT; SOAKING SOLUTION FOR FREEZING ALSO INCLUDED 20% ETHYLENE GLYCOL.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 %PEG80001reservoir
2200 mM1reservoirMgCl2
3100 mMMOPSO1reservoir
41 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.16→23.3 Å / Num. obs: 49688 / % possible obs: 91.5 % / Observed criterion σ(I): -2 / Redundancy: 5.4 % / Rsym value: 0.052 / Net I/σ(I): 8
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.444 / % possible all: 70.3
Reflection
*PLUS
Num. measured all: 268076 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 70.3 % / Rmerge(I) obs: 0.469

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Processing

Software
NameClassification
AMoREphasing
MLPHAREphasing
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 5EAS

5eas


Resolution: 2.15→22 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
Details: THE PROTEIN CONSISTS OF RESIDUES 1 - 548. RESIDUES 1 - 20 ARE ABSENT FROM THE ELECTRON DENSITY. RESIDUES 97 - 102 EXHIBIT WEAK DENSITY, AND MAY BE IN MULTIPLE CONFORMATIONS. RESIDUES 315 - ...Details: THE PROTEIN CONSISTS OF RESIDUES 1 - 548. RESIDUES 1 - 20 ARE ABSENT FROM THE ELECTRON DENSITY. RESIDUES 97 - 102 EXHIBIT WEAK DENSITY, AND MAY BE IN MULTIPLE CONFORMATIONS. RESIDUES 315 - 333 EXHIBIT ANISOTROPIC ELECTRON DENSITY. RESIDUES 524 - 528 ARE ABSENT FROM THE ELECTRON DENSITY. MUCH OF THE FARNESYL CHAIN OF THE BOUND SUBSTRATE ANALOG IS DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2337 5 %RANDOM
Rwork0.242 ---
obs0.242 48439 89.21 %-
Displacement parametersBiso mean: 40.7 Å2
Refinement stepCycle: LAST / Resolution: 2.15→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4246 0 29 135 4410
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.098
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.982
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.15→2.25 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.46 230 3.44 %
Rwork0.39 4833 -
obs--75.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.982

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