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

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Basic information

Entry
Database: PDB / ID: 4kvw
TitleCrystal structure of Aspergillus terreus aristolochene synthase complexed with (3R,6R,9aR)-6,9a-dimethyl-3-(prop-1-en-2-yl)decahydroquinolizin-5-ium
ComponentsAristolochene synthase
KeywordsLYASE/LYASE INHIBITOR / Class I terpenoid cyclase / alpha-helical fold / farnesyl diphosphate / 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-JF4 / PYROPHOSPHATE 2- / Aristolochene synthase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 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)146,89926
Polymers144,8864
Non-polymers2,01322
Water17,655980
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 area3380 Å2
ΔGint-68 kcal/mol
Surface area24920 Å2
MethodPISA
2
C: Aristolochene synthase
D: 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 area3330 Å2
ΔGint-69 kcal/mol
Surface area25140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.393, 124.393, 202.857
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, 1002 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-JF4 / (3R,5S,6R,9aR)-6,9a-dimethyl-3-(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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 980 / 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: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
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 (100 mM ...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 (100 mM magnesium formate, 12% 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: 2.1→50 Å / Num. obs: 105819 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 19.292
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.702 / % possible all: 100

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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: 2.102→50 Å / SU ML: 0.23 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.06 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 5287 5 %RANDOM
Rwork0.1944 ---
obs0.1944 105808 99.5 %-
all-106337 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.102→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9816 0 120 980 10916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210169
X-RAY DIFFRACTIONf_angle_d0.68713783
X-RAY DIFFRACTIONf_chiral_restr0.0461509
X-RAY DIFFRACTIONf_plane_restr0.0031761
X-RAY DIFFRACTIONf_dihedral_angle_d14.2373851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.102-2.12560.31071570.24333089X-RAY DIFFRACTION93
2.1256-2.15060.32271740.23843323X-RAY DIFFRACTION100
2.1506-2.17680.28171750.23413360X-RAY DIFFRACTION100
2.1768-2.20430.28191710.24253275X-RAY DIFFRACTION100
2.2043-2.23340.30451610.22973341X-RAY DIFFRACTION100
2.2334-2.26390.2691860.22513335X-RAY DIFFRACTION100
2.2639-2.29630.27241780.21693313X-RAY DIFFRACTION100
2.2963-2.33060.23141760.21843318X-RAY DIFFRACTION100
2.3306-2.3670.26491710.21923332X-RAY DIFFRACTION100
2.367-2.40580.2841860.20943310X-RAY DIFFRACTION100
2.4058-2.44730.24981500.2143400X-RAY DIFFRACTION100
2.4473-2.49180.26321730.22143285X-RAY DIFFRACTION100
2.4918-2.53970.28771770.21623360X-RAY DIFFRACTION100
2.5397-2.59150.27371720.21143363X-RAY DIFFRACTION100
2.5915-2.64790.25591740.21693314X-RAY DIFFRACTION100
2.6479-2.70950.26761740.21533321X-RAY DIFFRACTION100
2.7095-2.77720.24461800.21333350X-RAY DIFFRACTION100
2.7772-2.85230.25361870.2083329X-RAY DIFFRACTION100
2.8523-2.93620.25341890.21083340X-RAY DIFFRACTION100
2.9362-3.0310.23061860.22583369X-RAY DIFFRACTION100
3.031-3.13930.25181740.21443330X-RAY DIFFRACTION100
3.1393-3.26490.24382030.21383357X-RAY DIFFRACTION100
3.2649-3.41350.21881720.20943339X-RAY DIFFRACTION100
3.4135-3.59340.26551610.20493408X-RAY DIFFRACTION100
3.5934-3.81840.21461760.18743381X-RAY DIFFRACTION100
3.8184-4.11310.19291910.16233400X-RAY DIFFRACTION100
4.1131-4.52680.16531740.1453374X-RAY DIFFRACTION100
4.5268-5.18110.19061890.15333444X-RAY DIFFRACTION100
5.1811-6.5250.17771770.17013458X-RAY DIFFRACTION100
6.525-47.5840.15131730.15093603X-RAY DIFFRACTION100

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