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Yorodumi- PDB-3lz9: The Crystal Structure of 5-epi-aristolochene synthase M4 mutant c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lz9 | ||||||
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Title | The Crystal Structure of 5-epi-aristolochene synthase M4 mutant complexed with (2-trans,6-trans)-2-fluorofarnesyl diphosphate | ||||||
Components | Aristolochene synthase | ||||||
Keywords | LYASE / plant terpenoid cyclase / 5-epi-aristolochene synthase / metal-binding domain / (2-trans / 6-trans)-2-fluorofarnesyl diphosphate / Cytoplasm / Magnesium / Metal-binding | ||||||
Function / homology | Function and homology information 5-epiaristolochene synthase / 5-epi-aristolochene synthase activity / sesquiterpene biosynthetic process / diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Nicotiana tabacum (common tobacco) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å | ||||||
Authors | Noel, J.P. / Dellas, N. / Faraldos, J.A. / Zhao, M. / Hess Jr., B.A. / Smentek, L. / Coates, R.M. / O'Maille, P.E. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2010 Title: Structural elucidation of cisoid and transoid cyclization pathways of a sesquiterpene synthase using 2-fluorofarnesyl diphosphates. Authors: Noel, J.P. / Dellas, N. / Faraldos, J.A. / Zhao, M. / Hess, B.A. / Smentek, L. / Coates, R.M. / O'Maille, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lz9.cif.gz | 122.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lz9.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 3lz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/3lz9 ftp://data.pdbj.org/pub/pdb/validation_reports/lz/3lz9 | HTTPS FTP |
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-Related structure data
Related structure data | 3m00C 3m01C 3m02C 5eatS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 63209.758 Da / Num. of mol.: 1 / Mutation: A274T, V372I, Y406L, V516I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: EAS3, EAS4 / Plasmid: pHis9GW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q40577, aristolochene synthase | ||
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#2: Chemical | ChemComp-FPF / ( | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% PEG 8000, 200 mM magnesium acetate, 100 mM MOPSO, pH 7.0, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2005 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→50 Å / Num. obs: 30872 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.72 % / Biso Wilson estimate: 45.03 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.99 |
Reflection shell | Resolution: 2.28→2.38 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 3.7 / Num. measured obs: 30872 / Num. unique all: 5406 / Num. unique obs: 5064 / % possible all: 93.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5EAT Resolution: 2.28→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
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Solvent computation | Bsol: 45.693 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.5 Å2 / Biso mean: 51.852 Å2 / Biso min: 3.73 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.38 Å
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Xplor file |
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