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

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Basic information

Entry
Database: PDB / ID: 4kvd
TitleCrystal structure of Aspergillus terreus aristolochene synthase complexed with (4aS,7S)-1,4a-dimethyl-7-(prop-1-en-2-yl)decahydroquinolin-1-ium
ComponentsAristolochene synthase
KeywordsLYASE/LYASE INHIBITOR / Class I terpene cyclase / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


aristolochene synthase / aristolochene synthase activity / small molecule metabolic process / metal ion binding
Similarity search - Function
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-1SS / PYROPHOSPHATE 2- / Aristolochene synthase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChen, M. / Faraldos, J.A. / Al-lami, N. / Janvier, M. / D'Antonio, E.L. / 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 22, 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)147,10729
Polymers144,8864
Non-polymers2,22225
Water17,655980
1
A: Aristolochene synthase
B: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,65816
Polymers72,4432
Non-polymers1,21514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-70 kcal/mol
Surface area25000 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 area3310 Å2
ΔGint-68 kcal/mol
Surface area25220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.788, 122.788, 202.532
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, 1005 molecules

#2: Chemical
ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


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.: 13 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-1SS / (1R,4aS,7S,8aR)-1,4a-dimethyl-7-(prop-1-en-2-yl)decahydroquinolinium


Mass: 208.363 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H26N
#6: Water ChemComp-HOH / water / 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: 3.04 Å3/Da / Density % sol: 59.57 %
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 (100 mM Bis- ...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 Bis-Tris, pH 7.0, 200 mM lithium sulfate, 27% 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: X25 / Wavelength: 1.075 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2012
Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification
RadiationMonochromator: Double crystal Si(111) with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally focusing at 3.3:1 demagnification
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 69660 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 30
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 9.333 / Rsym value: 0.277 / % 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 2OA6

2oa6


Resolution: 2.4→50 Å / SU ML: 0.24 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.99 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 3517 5.05 %random
Rwork0.1743 ---
obs0.1743 69619 99.9 %-
all-69702 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9816 0 133 980 10929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510152
X-RAY DIFFRACTIONf_angle_deg0.813752
X-RAY DIFFRACTIONf_dihedral_angle_d213836
X-RAY DIFFRACTIONf_improper_angle_d1.11504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.43320.25351380.19372610X-RAY DIFFRACTION100
2.4332-2.46790.27761360.20052654X-RAY DIFFRACTION100
2.4679-2.50470.2771420.19822595X-RAY DIFFRACTION100
2.5047-2.54390.25351420.18992587X-RAY DIFFRACTION100
2.5439-2.58560.24151350.192600X-RAY DIFFRACTION100
2.5856-2.63020.23091800.19282608X-RAY DIFFRACTION100
2.6302-2.6780.26281420.19342602X-RAY DIFFRACTION100
2.678-2.72950.28441220.19372662X-RAY DIFFRACTION100
2.7295-2.78520.26721460.19032598X-RAY DIFFRACTION100
2.7852-2.84580.26151250.18712627X-RAY DIFFRACTION100
2.8458-2.91190.24191480.1942604X-RAY DIFFRACTION100
2.9119-2.98480.24441520.19462621X-RAY DIFFRACTION100
2.9848-3.06540.23561350.19522650X-RAY DIFFRACTION100
3.0654-3.15560.22511340.18872634X-RAY DIFFRACTION100
3.1556-3.25750.23291200.19612630X-RAY DIFFRACTION100
3.2575-3.37390.25431290.1822654X-RAY DIFFRACTION100
3.3739-3.50890.20691430.17642643X-RAY DIFFRACTION100
3.5089-3.66850.1971490.17152635X-RAY DIFFRACTION100
3.6685-3.86190.18541400.15872662X-RAY DIFFRACTION100
3.8619-4.10370.16691310.14782657X-RAY DIFFRACTION100
4.1037-4.42030.17551380.14372669X-RAY DIFFRACTION100
4.4203-4.86470.16351580.14542668X-RAY DIFFRACTION100
4.8647-5.56770.19981320.16892704X-RAY DIFFRACTION100
5.5677-7.0110.19781460.17692711X-RAY DIFFRACTION100
7.011-47.08380.15721540.15542817X-RAY DIFFRACTION99

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