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Yorodumi- PDB-5zfj: Crystal structure of a cyclase Filc from Fischerella sp. in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zfj | ||||||
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Title | Crystal structure of a cyclase Filc from Fischerella sp. in complex with 4-(1H-Indol-3-yl)butan-2-one | ||||||
Components | acyclase | ||||||
Keywords | TRANSFERASE / prenyltransferase | ||||||
Function / homology | 4-(1~{H}-indol-3-yl)butan-2-one / DI(HYDROXYETHYL)ETHER / 12-epi-hapalindole U synthase Function and homology information | ||||||
Biological species | Mastigocladus laminosus UTEX LB 1931 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 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 | 5zfj.cif.gz | 188.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zfj.ent.gz | 146.2 KB | Display | PDB format |
PDBx/mmJSON format | 5zfj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/5zfj ftp://data.pdbj.org/pub/pdb/validation_reports/zf/5zfj | HTTPS FTP |
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-Related structure data
Related structure data | 5yvkSC 5yvlC 5yvpC 5z53C 5z54C 6a8xC 6a92C 6a98C 6a99C 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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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 24705.799 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mastigocladus laminosus UTEX LB 1931 (bacteria) Strain: UTEX LB 1931 / Gene: filC1 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1P8VSI6 |
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-Non-polymers , 6 types, 789 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-9BF / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | This sequence is from ncbi with protein id APZ79579.1. |
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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: 2.06 Å3/Da / Density % sol: 40.26 % / Mosaicity: 0.621 ° |
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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: TPS 05A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 4, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: LN2 cooled Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.86→25 Å / Num. obs: 69836 / % possible obs: 99.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.031 / Rrim(I) all: 0.085 / Χ2: 0.715 / Net I/σ(I): 6.8 / Num. measured all: 513137 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YVK Resolution: 1.86→24.66 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.65 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.124 / 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: 31.201 Å2
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Refinement step | Cycle: 1 / Resolution: 1.86→24.66 Å
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Refine LS restraints |
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