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- PDB-3cke: Crystal structure of aristolochene synthase in complex with 12,13... -

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Basic information

Entry
Database: PDB / ID: 3cke
TitleCrystal structure of aristolochene synthase in complex with 12,13-difluorofarnesyl diphosphate
ComponentsAristolochene synthase
KeywordsLYASE / substrate binding / metal ion binding / catalysis / conformational changes
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
BETA-MERCAPTOETHANOL / Chem-FDF / PYROPHOSPHATE 2- / Aristolochene synthase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsShishova, E.Y. / Yu, F. / Miller, D.J. / Faraldos, J.A. / Zhao, Y. / Coates, R.M. / Allemann, R.K. / Cane, D.E. / Christianson, D.W.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: X-ray Crystallographic Studies of Substrate Binding to Aristolochene Synthase Suggest a Metal Ion Binding Sequence for Catalysis.
Authors: Shishova, E.Y. / Yu, F. / Miller, D.J. / Faraldos, J.A. / Zhao, Y. / Coates, R.M. / Allemann, R.K. / Cane, D.E. / Christianson, D.W.
History
DepositionMar 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)147,85814
Polymers146,0954
Non-polymers1,76310
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aristolochene synthase
B: Aristolochene synthase
D: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,82411
Polymers109,5713
Non-polymers1,2538
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-9.5 kcal/mol
Surface area27200 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-10.1 kcal/mol
Surface area28620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.534, 146.842, 84.110
Angle α, β, γ (deg.)90.00, 97.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aristolochene synthase


Mass: 36523.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: Ari1 / Plasmid: pET11-rASA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9UR08, aristolochene synthase

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Non-polymers , 7 types, 253 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FDF / (2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate


Mass: 418.307 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H26F2O7P2
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#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: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 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 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→56.3 Å / Num. all: 57488 / Num. obs: 57488 / % possible obs: 99.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.3
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.649 / % possible all: 0.998

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2E4O

2e4o


Resolution: 2.4→56.3 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.29 5804 RANDOM
Rwork0.245 --
all0.29 57035 -
obs-57035 -
Refinement stepCycle: LAST / Resolution: 2.4→56.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9490 0 104 243 9837
LS refinement shellHighest resolution: 2.4 Å / Rfactor Rfree: 0.387 / Rfactor Rwork: 0.333

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