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Yorodumi- PDB-5imi: Crystal structure of S303A Aspergillus terreus aristolochene synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5imi | ||||||
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Title | Crystal structure of S303A Aspergillus terreus aristolochene synthase complexed with (1S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)decahydroquinolizin-5-ium | ||||||
Components | Aristolochene synthase | ||||||
Keywords | LYASE/LYASE INHIBITOR / Lyase / terpene cyclases / 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 | ||||||
Biological species | Aspergillus terreus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.462 Å | ||||||
Authors | Chen, M. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2016 Title: Probing the Role of Active Site Water in the Sesquiterpene Cyclization Reaction Catalyzed by Aristolochene Synthase. Authors: Chen, M. / Chou, W.K. / Al-Lami, N. / Faraldos, J.A. / 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 | 5imi.cif.gz | 273 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5imi.ent.gz | 219.3 KB | Display | PDB format |
PDBx/mmJSON format | 5imi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5imi_validation.pdf.gz | 500.6 KB | Display | wwPDB validaton report |
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Full document | 5imi_full_validation.pdf.gz | 515.4 KB | Display | |
Data in XML | 5imi_validation.xml.gz | 50.7 KB | Display | |
Data in CIF | 5imi_validation.cif.gz | 70.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/5imi ftp://data.pdbj.org/pub/pdb/validation_reports/im/5imi | HTTPS FTP |
-Related structure data
Related structure data | 5imnC 5impC 5in8C 5ivgC 4kuxS C: citing same article (ref.) S: Starting model for refinement |
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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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3 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 36205.395 Da / Num. of mol.: 4 / Mutation: S303A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus terreus (mold) / Gene: Ari1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UR08, aristolochene synthase |
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-Non-polymers , 5 types, 623 molecules
#2: Chemical | ChemComp-POP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-JF1 / ( #5: Chemical | ChemComp-GOL / | #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: 3.12 Å3/Da / Density % sol: 60.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 200 mM ammonium acetate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→50 Å / Num. obs: 66366 / % possible obs: 100 % / Redundancy: 13.9 % / Net I/σ(I): 19.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KUX Resolution: 2.462→47.521 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.462→47.521 Å
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Refine LS restraints |
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LS refinement shell |
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