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

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Basic information

Entry
Database: PDB / ID: 4kvi
TitleCrystal structure of Aspergillus terreus aristolochene synthase complexed with (4aS,7S)-4a-methyl-7-(prop-1-en-2-yl)-2,3,4,4a,5,6,7,8-octahydroquinolin-1-ium
ComponentsAristolochene synthase
KeywordsLYASE/LYASE INHIBITOR / Class I terpene cyclase / alpha-helical fold / farnesyl diphosphate / metal-binding / magnesium / 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-1SV / PYROPHOSPHATE 2- / Aristolochene synthase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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)146,65024
Polymers144,8864
Non-polymers1,76520
Water16,069892
1
A: Aristolochene synthase
B: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,32512
Polymers72,4432
Non-polymers88210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-67 kcal/mol
Surface area24900 Å2
MethodPISA
2
C: Aristolochene synthase
D: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,32512
Polymers72,4432
Non-polymers88210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-68 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.397, 123.397, 201.605
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#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
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical
ChemComp-1SV / (4aS,7S)-4a-methyl-7-(prop-1-en-2-yl)-2,3,4,4a,5,6,7,8-octahydroquinolinium


Mass: 192.320 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H22N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 892 / 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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7
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 HEPES, ...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 HEPES, pH 7.7, 200 mM magnesium chloride, 23% 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: Jul 25, 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: 2.15→50 Å / Num. obs: 96118 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 16.304
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 3.25 / Rsym value: 0.569 / % possible all: 99.9

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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 4KVD

4kvd


Resolution: 2.15→50 Å / SU ML: 0.22 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.71 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 4811 5.01 %RANDOM
Rwork0.2083 ---
obs0.2083 96109 99 %-
all-97027 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9816 0 104 892 10812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510128
X-RAY DIFFRACTIONf_angle_deg0.813724
X-RAY DIFFRACTIONf_dihedral_angle_d20.93824
X-RAY DIFFRACTIONf_improper_angle_d1.511496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.17480.27491750.24393030X-RAY DIFFRACTION100
2.1748-2.20040.27891570.24193036X-RAY DIFFRACTION100
2.2004-2.22720.27391670.24243033X-RAY DIFFRACTION100
2.2272-2.25540.2811700.24032984X-RAY DIFFRACTION100
2.2554-2.28510.29871430.23983086X-RAY DIFFRACTION100
2.2851-2.31640.2571610.23443044X-RAY DIFFRACTION100
2.3164-2.34950.30961530.23183004X-RAY DIFFRACTION100
2.3495-2.38460.27461520.21963063X-RAY DIFFRACTION100
2.3846-2.42180.24411610.22453026X-RAY DIFFRACTION100
2.4218-2.46150.28651770.23573009X-RAY DIFFRACTION100
2.4615-2.5040.26521570.23783019X-RAY DIFFRACTION100
2.504-2.54950.24331630.23173040X-RAY DIFFRACTION100
2.5495-2.59850.27941450.22363060X-RAY DIFFRACTION100
2.5985-2.65160.29221720.24243006X-RAY DIFFRACTION100
2.6516-2.70920.27591790.23083003X-RAY DIFFRACTION100
2.7092-2.77220.29811540.233070X-RAY DIFFRACTION99
2.7722-2.84150.26751530.22583030X-RAY DIFFRACTION99
2.8415-2.91840.2271630.23233046X-RAY DIFFRACTION99
2.9184-3.00420.26361390.23413066X-RAY DIFFRACTION99
3.0042-3.10120.25221510.22663052X-RAY DIFFRACTION99
3.1012-3.2120.2521650.22913020X-RAY DIFFRACTION99
3.212-3.34060.23381520.23233078X-RAY DIFFRACTION99
3.3406-3.49250.25451700.21563017X-RAY DIFFRACTION99
3.4925-3.67660.25831580.20883045X-RAY DIFFRACTION99
3.6766-3.90690.19041600.18793034X-RAY DIFFRACTION99
3.9069-4.20830.20531780.17493016X-RAY DIFFRACTION98
4.2083-4.63150.18941780.16623058X-RAY DIFFRACTION98
4.6315-5.30090.22261340.17933071X-RAY DIFFRACTION98
5.3009-6.67560.23141730.18833081X-RAY DIFFRACTION97
6.6756-47.22150.17141510.15593171X-RAY DIFFRACTION96

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