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Yorodumi- PDB-3bny: Crystal structure of aristolochene synthase complexed with 2-fluo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bny | ||||||
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Title | Crystal structure of aristolochene synthase complexed with 2-fluorofarnesyl diphosphate (2F-FPP) | ||||||
Components | Aristolochene synthase | ||||||
Keywords | LYASE / sesquiterpene cyclase / isoprenoid / farnesyl diphosphate / magnesium / cyclization | ||||||
Function / homology | Function and homology information aristolochene synthase / aristolochene synthase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Aspergillus terreus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.89 Å | ||||||
Authors | Shishova, E.Y. / Christianson, D.W. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bny.cif.gz | 257.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bny.ent.gz | 208.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/3bny ftp://data.pdbj.org/pub/pdb/validation_reports/bn/3bny | HTTPS FTP |
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-Related structure data
Related structure data | 3bnxC 3ckeC 2e4oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | 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 , 5 types, 532 molecules
#2: Chemical | ChemComp-FPF / ( #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.6 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 18% PEG 6000, 100 mM Tris (pH 8.5), 0.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2006 Details: Platinum-coated 1:1 focusing toroidal mirror. Double silicon crystal monochromator. |
Radiation | Monochromator: Double silicon crystal monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→61.08 Å / Num. all: 104421 / Num. obs: 104421 / % possible obs: 88.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.89→1.96 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 3.2 / Num. unique all: 13457 / % possible all: 77.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2E4O Resolution: 1.89→22.33 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
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Displacement parameters | Biso mean: 31.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.89→22.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.96 Å
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