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Yorodumi- PDB-4okz: Selinadiene Synthase in complex with dihydrofarnesyl pyrophosphate -
+Open data
-Basic information
Entry | Database: PDB / ID: 4okz | ||||||
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Title | Selinadiene Synthase in complex with dihydrofarnesyl pyrophosphate | ||||||
Components | Terpene synthase metal-binding domain-containing protein | ||||||
Keywords | TRANSFERASE / Sesquiterpene / cyclase / terpenoid / induced fit / closed conformation / Dihydrofarnesyl pyrophosphate / pyrophosphate sensor | ||||||
Function / homology | Function and homology information selina-4(15),7(11)-diene synthase / terpene synthase activity / terpenoid biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Streptomyces pristinaespiralis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Baer, P. / Rabe, P. / Fischer, K. / Citron, C.A. / Klapschinski, T. / Groll, M. / Dickschat, J.S. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Induced-fit mechanism in class i terpene cyclases. Authors: Baer, P. / Rabe, P. / Fischer, K. / Citron, C.A. / Klapschinski, T.A. / Groll, M. / Dickschat, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4okz.cif.gz | 601.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4okz.ent.gz | 498.1 KB | Display | PDB format |
PDBx/mmJSON format | 4okz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4okz_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4okz_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 4okz_validation.xml.gz | 62.4 KB | Display | |
Data in CIF | 4okz_validation.cif.gz | 90.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/4okz ftp://data.pdbj.org/pub/pdb/validation_reports/ok/4okz | HTTPS FTP |
-Related structure data
Related structure data | 4okmSC 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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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 41283.453 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces pristinaespiralis (bacteria) Gene: SSDG_02809, ZP_06911744 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5HDJ6, squalene synthase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-3E9 / ( #4: 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: 2.48 Å3/Da / Density % sol: 50.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.1 M TRIS, 200 mM MgCl2, 24% PEG 3350, 1 mM dihydrofarnesyl pyrophosphate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2013 |
Radiation | Monochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 130090 / Num. obs: 129570 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 4.3 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4OKM Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.487 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.674 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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