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- PDB-4kvy: Crystal structure of Aspergillus terreus aristolochene synthase c... -

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Basic information

Entry
Database: PDB / ID: 4kvy
TitleCrystal structure of Aspergillus terreus aristolochene synthase complexed with (1S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)decahydroquinolizin-5-ium
ComponentsAristolochene synthase
KeywordsLYASE/LYASE INHIBITOR / Class I terpenoid cyclase / alpha-helical fold / farnesyl diphosphate / metal-binding / magnesium / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


aristolochene synthase / aristolochene synthase activity / isoprenoid biosynthetic process / metal ion binding
Similarity search - Function
Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-JF1 / PYROPHOSPHATE 2- / Aristolochene synthase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChen, M. / Al-lami, N. / Janvier, M. / D'Antonio, E.L. / Faraldos, J.A. / Cane, D.E. / Allemann, R.K. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2013
Title: Mechanistic insights from the binding of substrate and carbocation intermediate analogues to aristolochene synthase.
Authors: Chen, M. / Al-Lami, N. / Janvier, M. / D'Antonio, E.L. / Faraldos, J.A. / Cane, D.E. / Allemann, R.K. / Christianson, D.W.
History
DepositionMay 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 20, 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 / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_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_asym_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: Aristolochene synthase
B: Aristolochene synthase
C: Aristolochene synthase
D: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,80725
Polymers144,8864
Non-polymers1,92121
Water19,4021077
1
A: Aristolochene synthase
B: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,44913
Polymers72,4432
Non-polymers1,00711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-67 kcal/mol
Surface area24810 Å2
MethodPISA
2
C: Aristolochene synthase
D: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,35712
Polymers72,4432
Non-polymers91410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-68 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.251, 124.251, 202.997
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, 4 molecules ABCD

#1: Protein
Aristolochene synthase / AS / Sesquiterpene cyclase


Mass: 36221.395 Da / Num. of mol.: 4 / Fragment: UNP residues 14-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: Ari1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9UR08, aristolochene synthase

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Non-polymers , 5 types, 1098 molecules

#2: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-JF1 / (1S,5S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)octahydro-2H-quinolizinium


Mass: 208.363 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H26N
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1077 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3 uL protein (10 mg/mL ATAS, 20 mM MES, pH 6.5, 1.9 mM magnesium chloride, 120 mM sodium chloride, 3 mM BME, 1.6 mM sodium pyrophosphate, 1.5 mM inhibitor) + 3 uL precipitant (2% Tacsimate, ...Details: 3 uL protein (10 mg/mL ATAS, 20 mM MES, pH 6.5, 1.9 mM magnesium chloride, 120 mM sodium chloride, 3 mM BME, 1.6 mM sodium pyrophosphate, 1.5 mM inhibitor) + 3 uL precipitant (2% Tacsimate, pH 6.0, 100 mM Bis-Tris, pH 7.0, 16% w/v PEG3350) against 500 uL precipitant, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2012
Details: Cryogenically cooled double crystal monochromator with horizontally focusing sagitally bent second crystal with 4:1 magnification ratio and vertically focusing mirror
RadiationMonochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 132057 / Num. obs: 130831 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 14.15
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.68 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASER(CCP4i)phasing
PHENIX(phenix.refine: dev_1370)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KVI

4kvi


Resolution: 1.95→50 Å / SU ML: 0.23 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.24 6591 5.04 %RANDOM
Rwork0.19 ---
obs0.19 130821 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9816 0 114 1077 11007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610155
X-RAY DIFFRACTIONf_angle_d1.00913764
X-RAY DIFFRACTIONf_chiral_restr0.071507
X-RAY DIFFRACTIONf_plane_restr0.0051759
X-RAY DIFFRACTIONf_dihedral_angle_d15.4533845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97370.29741900.26763812X-RAY DIFFRACTION92
1.9737-1.99690.30742150.24824034X-RAY DIFFRACTION99
1.9969-2.02120.30032170.23594099X-RAY DIFFRACTION99
2.0212-2.04680.28742260.2314091X-RAY DIFFRACTION99
2.0468-2.07380.29452270.22364111X-RAY DIFFRACTION99
2.0738-2.10220.25692300.21054072X-RAY DIFFRACTION99
2.1022-2.13220.26092020.20984125X-RAY DIFFRACTION99
2.1322-2.1640.25192230.2074083X-RAY DIFFRACTION99
2.164-2.19780.27132220.21414118X-RAY DIFFRACTION99
2.1978-2.23390.26392070.20414119X-RAY DIFFRACTION99
2.2339-2.27240.27882300.20114094X-RAY DIFFRACTION99
2.2724-2.31370.24062160.20274134X-RAY DIFFRACTION99
2.3137-2.35820.26391970.20074128X-RAY DIFFRACTION99
2.3582-2.40640.28952390.19854102X-RAY DIFFRACTION100
2.4064-2.45870.25782140.20094125X-RAY DIFFRACTION99
2.4587-2.51590.26232260.20374139X-RAY DIFFRACTION99
2.5159-2.57880.26652240.20614106X-RAY DIFFRACTION99
2.5788-2.64850.26982210.21554192X-RAY DIFFRACTION100
2.6485-2.72640.26841990.21314139X-RAY DIFFRACTION100
2.7264-2.81440.22562030.20474198X-RAY DIFFRACTION100
2.8144-2.9150.26182070.20944145X-RAY DIFFRACTION100
2.915-3.03170.2812720.22284151X-RAY DIFFRACTION100
3.0317-3.16960.25982290.21494160X-RAY DIFFRACTION100
3.1696-3.33670.27562070.20854149X-RAY DIFFRACTION100
3.3367-3.54570.23032090.19954227X-RAY DIFFRACTION100
3.5457-3.81940.21122470.18234177X-RAY DIFFRACTION100
3.8194-4.20350.18891940.15394249X-RAY DIFFRACTION100
4.2035-4.81130.17632440.14044206X-RAY DIFFRACTION100
4.8113-6.05970.18722190.15764300X-RAY DIFFRACTION100
6.0597-47.55070.18672350.14944445X-RAY DIFFRACTION99

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