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Yorodumi- PDB-6wkh: Crystal structure of pentalenene synthase mutant F76W complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wkh | ||||||
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Title | Crystal structure of pentalenene synthase mutant F76W complexed with 12,13-difluorofarnesyl diphosphate | ||||||
Components | Pentalenene synthase | ||||||
Keywords | METAL BINDING PROTEIN / LYASE/INHIBITOR / Terpene synthase / terpene synthase fold / sesquiterpene / fluoro analog / metal binding / LYASE-INHIBITOR complex | ||||||
Function / homology | pentalenene synthase / pentalenene synthase activity / Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / antibiotic biosynthetic process / Isoprenoid synthase domain superfamily / metal ion binding / Chem-FDF / Pentalenene synthase Function and homology information | ||||||
Biological species | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Prem Kumar, R. / Matos, J.O. / Oprian, D.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2020 Title: Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase. Authors: Matos, J.O. / Kumar, R.P. / Ma, A.C. / Patterson, M. / Krauss, I.J. / Oprian, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wkh.cif.gz | 125.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wkh.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/6wkh ftp://data.pdbj.org/pub/pdb/validation_reports/wk/6wkh | HTTPS FTP |
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-Related structure data
Related structure data | 6wkcC 6wkdC 6wkeC 6wkfC 6wkgC 6wkiC 6wkjC 1ps1S 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
#1: Protein | Mass: 38089.445 Da / Num. of mol.: 2 / Mutation: F76W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: penA / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q55012, pentalenene synthase #2: Chemical | ChemComp-FDF / ( | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.69 Å3/Da / Density % sol: 66.69 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 0.8-1.2 M sodium tartrate, 100 mM Tris, and 5 mM DTT PH range: 7.5 - 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2019 / Details: Mirrors |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→20 Å / Num. obs: 36655 / % possible obs: 99.8 % / Redundancy: 19.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.137 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 20.2 % / Rmerge(I) obs: 1.67 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5340 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PS1 Resolution: 2.55→19.886 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.23 / 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 max: 152.81 Å2 / Biso mean: 72.7236 Å2 / Biso min: 34.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→19.886 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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