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

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Basic information

Entry
Database: PDB / ID: 4kwd
TitleCrystal structure of Aspergillus terreus aristolochene synthase complexed with (1R,8R,9aS)-1,9a-dimethyl-8-(prop-1-en-2-yl)decahydroquinolizin-5-ium
ComponentsAristolochene synthase
KeywordsLYASE/LYASE INHIBITOR / Class I terpene cyclase / metal-binding motif / farnesyl diphosphate / alpha-helical fold / 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-JF2 / PYROPHOSPHATE 2- / Aristolochene synthase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.857 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
Water18,8981049
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 area3340 Å2
ΔGint-68 kcal/mol
Surface area25020 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 area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.865, 123.865, 202.081
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, 1071 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-JF2 / (1R,5R,8R,9aS)-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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1049 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
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 (200 mM sodium ...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 (200 mM sodium malonate, pH 7.0, 15% 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: 1.857→50 Å / Num. obs: 151240 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 17.519
Reflection shellResolution: 1.857→1.93 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.781 / Rsym value: 0.763 / % 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: 1.857→47.374 Å / SU ML: 0.23 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.8 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 7536 5.03 %RANDOM
Rwork0.1934 ---
obs0.1934 150235 99.8 %-
all-150553 --
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 error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.857→47.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9816 0 120 1049 10985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01510160
X-RAY DIFFRACTIONf_angle_d1.51313769
X-RAY DIFFRACTIONf_chiral_restr0.121507
X-RAY DIFFRACTIONf_plane_restr0.0081759
X-RAY DIFFRACTIONf_dihedral_angle_d16.7153847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.857-1.87830.31872530.27584822X-RAY DIFFRACTION100
1.8783-1.90040.32412610.25844680X-RAY DIFFRACTION100
1.9004-1.92360.30992470.25454697X-RAY DIFFRACTION100
1.9236-1.94790.28072900.23964716X-RAY DIFFRACTION100
1.9479-1.97350.29292700.2384767X-RAY DIFFRACTION100
1.9735-2.00060.30882510.22884731X-RAY DIFFRACTION100
2.0006-2.02920.26282450.22614739X-RAY DIFFRACTION100
2.0292-2.05940.25962440.22314791X-RAY DIFFRACTION100
2.0594-2.09160.27222660.21164696X-RAY DIFFRACTION100
2.0916-2.12590.25492420.20914759X-RAY DIFFRACTION100
2.1259-2.16260.22432540.20014731X-RAY DIFFRACTION100
2.1626-2.20190.23932600.20194759X-RAY DIFFRACTION100
2.2019-2.24430.22392620.20084729X-RAY DIFFRACTION100
2.2443-2.29010.24562480.20244799X-RAY DIFFRACTION100
2.2901-2.33990.24132660.20214726X-RAY DIFFRACTION100
2.3399-2.39430.23582380.19094788X-RAY DIFFRACTION100
2.3943-2.45420.23782500.19334769X-RAY DIFFRACTION100
2.4542-2.52050.2262510.20114793X-RAY DIFFRACTION100
2.5205-2.59470.24662360.19724769X-RAY DIFFRACTION100
2.5947-2.67840.24312480.20844792X-RAY DIFFRACTION100
2.6784-2.77410.25622300.21034796X-RAY DIFFRACTION100
2.7741-2.88520.23842270.20224814X-RAY DIFFRACTION100
2.8852-3.01650.25192560.21714811X-RAY DIFFRACTION100
3.0165-3.17550.26352560.21424804X-RAY DIFFRACTION100
3.1755-3.37440.22272470.20974802X-RAY DIFFRACTION100
3.3744-3.63480.21422390.19784872X-RAY DIFFRACTION100
3.6348-4.00050.21242650.17244823X-RAY DIFFRACTION100
4.0005-4.57890.17572400.14844883X-RAY DIFFRACTION100
4.5789-5.76730.1832790.15134891X-RAY DIFFRACTION100
5.7673-47.38970.14552800.14655081X-RAY DIFFRACTION100

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