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Yorodumi- PDB-4kvy: Crystal structure of Aspergillus terreus aristolochene synthase c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kvy | ||||||
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Title | Crystal structure of 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 / Class I terpenoid 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 | ||||||
Biological species | Aspergillus terreus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Chen, M. / Al-lami, N. / Janvier, M. / D'Antonio, E.L. / Faraldos, J.A. / Cane, D.E. / Allemann, R.K. / Christianson, D.W. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kvy.cif.gz | 279.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kvy.ent.gz | 224.9 KB | Display | PDB format |
PDBx/mmJSON format | 4kvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kvy_validation.pdf.gz | 495.1 KB | Display | wwPDB validaton report |
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Full document | 4kvy_full_validation.pdf.gz | 507.2 KB | Display | |
Data in XML | 4kvy_validation.xml.gz | 54.9 KB | Display | |
Data in CIF | 4kvy_validation.cif.gz | 80.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/4kvy ftp://data.pdbj.org/pub/pdb/validation_reports/kv/4kvy | HTTPS FTP |
-Related structure data
Related structure data | 4kuxC 4kvdC 4kviSC 4kvwC 4kwdC 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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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | 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 |
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-Non-polymers , 5 types, 1098 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: 60.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 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 (2% Tacsimate, ...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 (2% Tacsimate, pH 6.0, 100 mM Bis-Tris, pH 7.0, 16% w/v PEG3350) against 500 uL precipitant, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-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: Oct 19, 2012 Details: Cryogenically cooled double crystal monochromator with horizontally focusing sagitally bent second crystal with 4:1 magnification ratio and vertically focusing mirror |
Radiation | Monochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 132057 / Num. obs: 130831 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 14.15 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.68 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4KVI Resolution: 1.95→50 Å / SU ML: 0.23 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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LS refinement shell |
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