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- PDB-5eat: 5-EPI-ARISTOLOCHENE SYNTHASE FROM NICOTIANA TABACUM WITH SUBSTRAT... -

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Basic information

Entry
Database: PDB / ID: 5eat
Title5-EPI-ARISTOLOCHENE SYNTHASE FROM NICOTIANA TABACUM WITH SUBSTRATE ANALOG FARNESYL HYDROXYPHOSPHONATE
Components5-EPI-ARISTOLOCHENE SYNTHASE
KeywordsISOPRENOID SYNTHASE / ISOPRENOID CYCLASE / 5-EPI-ARISTOLOCHENE SYNTHASE / ISOPRENOID BIOSYNTHESIS / NATURAL PRODUCTS BIOSYNTHESIS
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 ...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-FHP / 5-epi-aristolochene synthase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT/DIFFERENCE FOURIER MAPS / Resolution: 2.8 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: 1990
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
DepositionJul 24, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: 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 ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.process_site / _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 1.4May 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)63,4435
Polymers63,0671
Non-polymers3754
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.330, 126.330, 121.698
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: 63067.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Strain: NK326 / Cell line: BL21 / Plasmid: PET28B(+) / Species (production host): Escherichia coli / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FHP / 1-HYDROXY-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENE PHOSPHONIC ACID / FARNESYL HYDROXYPHOSPHONATE


Mass: 302.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H27O4P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 65 %
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, 2 MM FARNESYL HYDROXYPHOSPHONATE; SOAKING SOLUTION FOR FREEZING ALSO INCLUDED 20% ETHYLENE GLYCOL.
Crystal grow
*PLUS
pH: 7 / 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: Nov 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 24648 / % possible obs: 98.3 % / Observed criterion σ(I): -2 / Redundancy: 5.5 % / Rsym value: 0.152 / Net I/σ(I): 5.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.531 / % possible all: 96.3
Reflection
*PLUS
Num. measured all: 136072 / Rmerge(I) obs: 0.187
Reflection shell
*PLUS
% possible obs: 96.3 % / Rmerge(I) obs: 0.531

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT/DIFFERENCE FOURIER MAPS
Starting model: NATIVE TEAS (PDB ENTRY 5EAS)

5eas


Resolution: 2.8→100 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
Details: THE PROTEIN CONSISTS OF RESIDUES 1 - 548. RESIDUES 1 - 16 ARE ABSENT FROM THE ELECTRON DENSITY. RESIDUES 17 - 24 ARE MODELED, BUT EXHIBIT WEAK DENSITY. RESIDUES 97 - 102 EXHIBIT WEAK DENSITY ...Details: THE PROTEIN CONSISTS OF RESIDUES 1 - 548. RESIDUES 1 - 16 ARE ABSENT FROM THE ELECTRON DENSITY. RESIDUES 17 - 24 ARE MODELED, BUT EXHIBIT WEAK DENSITY. RESIDUES 97 - 102 EXHIBIT WEAK DENSITY AND MAY BE IN MULTIPLE CONFORMATIONS. RESIDUES 315 - 333 EXHIBIT ANISOTROPIC ELECTRON DENSITY. RESIDUES 522 - 532 WERE DISORDERED IN THE NATIVE STRUCTURE (5EAS) BUT DISPLAY STRONG DENSITY IN THE FARNESYL HYDROXYPHOSPHONATE COMPLEX. RESIDUES 253 - 266 ARE BETTER ORDERED THAN IN THE NATIVE STRUCTURE, AND HAVE TRANSLATED 2-3 ANGSTROMS TOWARD THE ACTIVE SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1072 5 %RANDOM
Rwork0.24 ---
obs0.24 24664 94.9 %-
Displacement parametersBiso mean: 28.2 Å2
Refinement stepCycle: LAST / Resolution: 2.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4325 0 23 150 4498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.29
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.99
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: 2.8→2.93 Å / Rfactor Rfree error: 0.08 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.34 127 4.18 %
Rwork0.32 2667 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.HPHTOPPAR.HPH
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.99

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