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Yorodumi- PDB-6a99: Crystal structure of a Stig cyclases Fisc from Fischerella sp. TA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a99 | ||||||
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Title | Crystal structure of a Stig cyclases Fisc from Fischerella sp. TAU in complex with (3Z)-3-(1-methyl-2-pyrrolidinylidene)-3H-indole | ||||||
Components | aromatic prenyltransferase | ||||||
Keywords | TRANSFERASE / prenyltransferase | ||||||
Function / homology | metal ion binding / (3~{Z})-3-(1-methylpyrrolidin-2-ylidene)indole / FisC Function and homology information | ||||||
Biological species | Fischerella sp. UTEX 'LB 1931' (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Hu, X.Y. / Liu, W.D. / Chen, C.C. / Guo, R.T. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018 Title: The Crystal Structure of a Class of Cyclases that Catalyze the Cope Rearrangement Authors: Chen, C.C. / Hu, X. / Tang, X. / Yang, Y. / Ko, T.P. / Gao, J. / Zheng, Y. / Huang, J.W. / Yu, Z. / Li, L. / Han, S. / Cai, N. / Zhang, Y. / Liu, W. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a99.cif.gz | 174.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a99.ent.gz | 135.5 KB | Display | PDB format |
PDBx/mmJSON format | 6a99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a99_validation.pdf.gz | 493 KB | Display | wwPDB validaton report |
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Full document | 6a99_full_validation.pdf.gz | 508 KB | Display | |
Data in XML | 6a99_validation.xml.gz | 32 KB | Display | |
Data in CIF | 6a99_validation.cif.gz | 43.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/6a99 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/6a99 | HTTPS FTP |
-Related structure data
Related structure data | 5yvkSC 5yvlC 5yvpC 5z53C 5z54C 5zfjC 6a8xC 6a92C 6a98C 6a9fC 6aduC 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: 24116.777 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fischerella sp. UTEX 'LB 1931' (bacteria) Gene: fisC / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1P8VSL7 #2: Chemical | ChemComp-9UL / ( #3: Chemical | ChemComp-CA / #4: Chemical | #5: 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: 2.05 Å3/Da / Density % sol: 40.13 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.0M sodium citrate, 0.1M Imidazole pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 19, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.29→25 Å / Num. obs: 36512 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.035 / Rrim(I) all: 0.074 / Χ2: 1.336 / Net I/σ(I): 12.5 / Num. measured all: 147545 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YVK Resolution: 2.29→24.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.353 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.242 / 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: 51.838 Å2
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Refinement step | Cycle: 1 / Resolution: 2.29→24.94 Å
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Refine LS restraints |
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