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Yorodumi- PDB-6tjz: Crystal structure of the SVS_A2 protein (W156Y mutant) from ances... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tjz | ||||||
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Title | Crystal structure of the SVS_A2 protein (W156Y mutant) from ancestral sequence reconstruction at 2.4 A resolution | ||||||
Components | SVS_variant_AS3 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Terpene cyclase / engineered enzyme | ||||||
Biological species | Streptomyces sp. CWA1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Rudraraju, R. / Schnell, R. / Schneider, G. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 Title: Engineering of Ancestors as a Tool to Elucidate Structure, Mechanism, and Specificity of Extant Terpene Cyclase. Authors: Schriever, K. / Saenz-Mendez, P. / Rudraraju, R.S. / Hendrikse, N.M. / Hudson, E.P. / Biundo, A. / Schnell, R. / Syren, P.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tjz.cif.gz | 139.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tjz.ent.gz | 109.4 KB | Display | PDB format |
PDBx/mmJSON format | 6tjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/6tjz ftp://data.pdbj.org/pub/pdb/validation_reports/tj/6tjz | HTTPS FTP |
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-Related structure data
Related structure data | 6tbdC 6thuC 6tivC 6tjaC 4okzS 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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Unit cell |
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-Components
#1: Protein | Mass: 40452.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. CWA1 (bacteria) / Production host: Escherichia coli (E. coli) / References: EC: 4.2.3.158 #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: 2.62 Å3/Da / Density % sol: 53.05 % / Description: rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.2M Na phosphate 0.1M Bis-Tris-Propane pH 6.3 18% PEG 3350 Cryoprotection: 0.2M Na phosphate 0.1M Bis-Tris-Propane pH 6.3 24% PEG 3350 5mM MgCl2 5 mM FPP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2019 / Details: KB mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40.66 Å / Num. obs: 34301 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 61.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.031 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3555 / CC1/2: 0.739 / Rpim(I) all: 0.353 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OKZ Resolution: 2.4→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.128 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.301 / ESU R Free: 0.218 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 156.37 Å2 / Biso mean: 63.92 Å2 / Biso min: 43.28 Å2
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Refinement step | Cycle: final / Resolution: 2.4→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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