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Yorodumi- PDB-6thu: Crystal structure of the SVS_A2 protein (A224I mutant) from ances... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6thu | ||||||
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Title | Crystal structure of the SVS_A2 protein (A224I mutant) from ancestral sequence reconstruction at 2.6 A resolution | ||||||
Components | SVS_AS10 variant | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Crystal structure of the design protein SVS_AS10 variant at 2.6 A resolution BIOSYNTHETIC PROTEIN | ||||||
Biological species | Streptomyces sp. CWA1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 | 6thu.cif.gz | 138 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6thu.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 6thu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6thu_validation.pdf.gz | 429.1 KB | Display | wwPDB validaton report |
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Full document | 6thu_full_validation.pdf.gz | 433.4 KB | Display | |
Data in XML | 6thu_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 6thu_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/6thu ftp://data.pdbj.org/pub/pdb/validation_reports/th/6thu | HTTPS FTP |
-Related structure data
Related structure data | 6tbdC 6tivC 6tjaC 6tjzC 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: 40517.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Artificial design protein. / 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 % / Description: rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Na phosphate 0.1M Bis-Tris-Propane pH 6.5 12% PEG 3350 Cryoprotection 0.2M Na phosphate 0.1M Bis-Tris-Propane pH 6.5 20% PEG 3350 5mM MgCl2 |
-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: 0.91842 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2019 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91842 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→43.02 Å / Num. obs: 26961 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.033 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.7 / Num. unique obs: 3237 / CC1/2: 0.801 / Rpim(I) all: 0.312 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OKZ Resolution: 2.6→43 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.38 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.534 / ESU R Free: 0.259 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: 166.11 Å2 / Biso mean: 61.674 Å2 / Biso min: 37.64 Å2
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Refinement step | Cycle: final / Resolution: 2.6→43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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