+Open data
-Basic information
Entry | Database: PDB / ID: 6wki | ||||||
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Title | Crystal structure of pentalenene synthase mutant F76H | ||||||
Components | Pentalenene synthase | ||||||
Keywords | METAL BINDING PROTEIN / LYASE / Terpene synthase / terpene synthase fold / sesquiterpene / fluoro analog / metal binding | ||||||
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 / Pentalenene synthase Function and homology information | ||||||
Biological species | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 | 6wki.cif.gz | 154.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wki.ent.gz | 97.3 KB | Display | PDB format |
PDBx/mmJSON format | 6wki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wki_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
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Full document | 6wki_full_validation.pdf.gz | 436.1 KB | Display | |
Data in XML | 6wki_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 6wki_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/6wki ftp://data.pdbj.org/pub/pdb/validation_reports/wk/6wki | HTTPS FTP |
-Related structure data
Related structure data | 6wkcC 6wkdC 6wkeC 6wkfC 6wkgC 6wkhC 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: 38041.387 Da / Num. of mol.: 2 / Mutation: F76H 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: 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: 3.53 Å3/Da / Density % sol: 65.16 % |
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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: 0.9774 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: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→20 Å / Num. obs: 44617 / % possible obs: 99.8 % / Redundancy: 20.4 % / Biso Wilson estimate: 52.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.111 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 20.5 % / Rmerge(I) obs: 1.79 / Mean I/σ(I) obs: 2 / Num. unique obs: 6448 / CC1/2: 0.708 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PS1 Resolution: 2.35→19.97 Å / SU ML: 0.3012 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5767 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 60.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→19.97 Å
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Refine LS restraints |
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LS refinement shell |
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