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- PDB-4rnq: Crystal structure of tobacco 5-epi-aristolochene synthase (TEAS) ... -

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Basic information

Entry
Database: PDB / ID: 4rnq
TitleCrystal structure of tobacco 5-epi-aristolochene synthase (TEAS) with anilinogeranyl diphosphate (AGPP) and geraniline
Components5-epi-aristolochene synthase5-epiaristolochene synthase
KeywordsLYASE / TEAS / 5-epi-aristolochene synthase / anilinogeranyl diphosphate (AGPP) / geraniline / terpene synthase
Function / homology
Function and homology information


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 cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / 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 cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / 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
Geraniline / Chem-A4S / ACETATE ION / DIPHOSPHATE / 5-epi-aristolochene synthase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsKoo, H.J. / Crenshaw, C.M. / Starks, C. / Spielmann, H.P. / Chappell, J. / Noel, J.P.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Formation of a Novel Macrocyclic Alkaloid from the Unnatural Farnesyl Diphosphate Analogue Anilinogeranyl Diphosphate by 5-Epi-Aristolochene Synthase.
Authors: Rising, K.A. / Crenshaw, C.M. / Koo, H.J. / Subramanian, T. / Chehade, K.A. / Starks, C. / Allen, K.D. / Andres, D.A. / Spielmann, H.P. / Noel, J.P. / Chappell, J.
History
DepositionOct 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-epi-aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1408
Polymers63,2021
Non-polymers9397
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.750, 126.750, 124.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 63201.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His-tag removed after purification / Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: EAS3, EAS4 / Plasmid: pH9GW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q40577, 5-epiaristolochene synthase

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Non-polymers , 6 types, 64 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-A4S / (2E,6E)-3,7-dimethyl-8-(phenylamino)octa-2,6-dien-1-yl trihydrogen diphosphate / anilinogeranyl diphosphate


Mass: 405.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25NO7P2
#4: Chemical ChemComp-1GA / Geraniline / (4E,8E)-4,8-dimethyl-2-azabicyclo[9.2.2]pentadeca-1(13),4,8,11,14-pentaene


Mass: 227.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N
#5: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.95 Å3/Da / Density % sol: 68.86 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1:1 protein:MOPSO7 100mM, MgOAc 100 mM, PEG8000 10%, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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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: Feb 5, 2014 / Details: mirrors
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: 2.47→56.46 Å / Num. all: 36960 / Num. obs: 35371 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.2 / Scaling rejects: 259
Reflection shellResolution: 2.47→2.56 Å / Redundancy: 4 % / Rmerge(I) obs: 0.997 / Mean I/σ(I) obs: 1.1 / Num. measured all: 11919 / Num. unique all: 3013 / % possible all: 79.6

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Processing

Software
NameVersionClassificationNB
Aimless0.2.17data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
BOSdata collection
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→51.072 Å / SU ML: 0.35 / σ(F): 1.33 / Phase error: 28.08 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2264 1767 5.01 %
Rwork0.1749 --
obs0.1775 35264 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.83 Å2 / Biso mean: 70.8133 Å2 / Biso min: 29.7 Å2
Refinement stepCycle: LAST / Resolution: 2.47→51.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 59 57 4465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084518
X-RAY DIFFRACTIONf_angle_d1.0456129
X-RAY DIFFRACTIONf_chiral_restr0.037683
X-RAY DIFFRACTIONf_plane_restr0.012774
X-RAY DIFFRACTIONf_dihedral_angle_d15.8611696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.47-2.53680.36421170.34282101221879
2.5368-2.61150.38391090.30892060216979
2.6115-2.69580.35331130.27062259237284
2.6958-2.79210.3061350.254326362771100
2.7921-2.90390.30081450.244126602805100
2.9039-3.0360.2991430.235726752818100
3.036-3.19610.24711440.222726562800100
3.1961-3.39630.30071410.208526772818100
3.3963-3.65840.25881470.188626832830100
3.6584-4.02650.20031350.155227062841100
4.0265-4.60880.1561450.128727122857100
4.6088-5.80530.18931430.132827662909100
5.8053-51.08310.1741500.12529063056100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8464-1.23190.40244.5646-0.13071.9835-0.0213-0.3346-0.2440.40590.07270.76050.1371-0.3366-0.05050.5423-0.0660.0720.3251-0.07760.597128.993455.148121.5471
21.67383.3071-0.32778.089-1.00969.09810.1945-0.5572-0.06060.90770.0393-0.67880.08741.1923-0.2570.48080.0577-0.12930.3807-0.06530.547350.70359.519125.9638
33.2972-1.2218-0.95893.29912.9046.63010.01810.01950.2146-0.11080.2294-0.7798-0.2070.5231-0.21250.3596-0.03870.04310.3434-0.08450.555652.650463.96019.4003
42.48810.0787-0.04055.7123-0.21092.4105-0.06090.1345-0.451-0.13040.21570.34520.277-0.0067-0.04840.3808-0.02830.04860.357-0.07750.521237.258254.462613.599
51.95850.0057-0.26453.71740.36931.13560.0385-0.13980.45690.1512-0.02531.3187-0.3127-0.4302-0.0010.50950.05490.14340.4921-0.11321.028118.511877.860922.0691
65.1016-0.1011-1.23374.9826-1.97678.6407-0.09540.46830.6407-0.5424-0.21470.196-0.7762-0.2610.13120.64860.0275-0.00850.277-0.11690.767831.723584.261315.8139
74.02230.65320.22163.92981.16042.57260.10340.45120.3431-0.21050.00170.3104-0.03650.0462-0.09510.37020.06120.0380.322-0.04930.580133.727671.459314.3867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 79 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 116 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 195 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 222 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 412 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 413 through 472 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 473 through 548 )A0

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