[English] 日本語
Yorodumi- PDB-4kvd: Crystal structure of Aspergillus terreus aristolochene synthase c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kvd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Aspergillus terreus aristolochene synthase complexed with (4aS,7S)-1,4a-dimethyl-7-(prop-1-en-2-yl)decahydroquinolin-1-ium | ||||||
Components | Aristolochene synthase | ||||||
Keywords | LYASE/LYASE INHIBITOR / Class I terpene cyclase / 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: 2.4 Å | ||||||
Authors | Chen, M. / Faraldos, J.A. / Al-lami, N. / Janvier, M. / D'Antonio, E.L. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4kvd.cif.gz | 278.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4kvd.ent.gz | 223.8 KB | Display | PDB format |
PDBx/mmJSON format | 4kvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kvd_validation.pdf.gz | 494.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4kvd_full_validation.pdf.gz | 504.2 KB | Display | |
Data in XML | 4kvd_validation.xml.gz | 53.4 KB | Display | |
Data in CIF | 4kvd_validation.cif.gz | 77.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/4kvd ftp://data.pdbj.org/pub/pdb/validation_reports/kv/4kvd | HTTPS FTP |
-Related structure data
Related structure data | 4kuxC 4kviC 4kvwC 4kvyC 4kwdC 2oa6S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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 |
---|
-Non-polymers , 5 types, 1005 molecules
#2: Chemical | ChemComp-POP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-1SS / ( #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.57 % |
---|---|
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 (100 mM Bis- ...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 (100 mM Bis-Tris, pH 7.0, 200 mM lithium sulfate, 27% w/v PEG3350) against 500 uL precipitant, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2012 Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification |
Radiation | Monochromator: Double crystal Si(111) with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally focusing at 3.3:1 demagnification Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 69660 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 9.333 / Rsym value: 0.277 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OA6 Resolution: 2.4→50 Å / SU ML: 0.24 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.99 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|