+Open data
-Basic information
Entry | Database: PDB / ID: 6j03 | ||||||
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Title | Crystal structure of a cyclase mutant in apo form | ||||||
Components | 12-epi-hapalindole U synthase | ||||||
Keywords | TRANSFERASE / prenyltransferase / mutation | ||||||
Function / homology | Chem-0HZ / 12-epi-hapalindole U synthase Function and homology information | ||||||
Biological species | Fischerella ambigua UTEX 1903 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Tang, X.K. / Liu, W.D. / Chen, C.C. / Guo, R.T. | ||||||
Citation | Journal: Rsc Adv / Year: 2019 Title: Structural insights into the calcium dependence of Stig cyclases. Authors: Tang, X.K. / Xue, J. / Yang, Y.Y. / Ko, T.P. / Chen, C.Y. / Dai, L.H. / Guo, R.T. / Zhang, Y.H. / Chen, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j03.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j03.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 6j03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/6j03 ftp://data.pdbj.org/pub/pdb/validation_reports/j0/6j03 | HTTPS FTP |
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-Related structure data
Related structure data | 5yvkS S: Starting model for refinement |
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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: 21744.029 Da / Num. of mol.: 1 / Fragment: UNP residues 35-234 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fischerella ambigua UTEX 1903 (bacteria) Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: V5TER4 |
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#2: Chemical | ChemComp-0HZ / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.49 % / Mosaicity: 0.208 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG3350, Tryptone, 0.1 M HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 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: 1.48→25 Å / Num. obs: 44964 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.022 / Rrim(I) all: 0.043 / Χ2: 0.795 / Net I/σ(I): 13.4 / Num. measured all: 168760 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YVK Resolution: 1.48→24.12 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.527 / SU ML: 0.026 / SU R Cruickshank DPI: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.045 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: 117.8 Å2 / Biso mean: 18.962 Å2 / Biso min: 10.91 Å2
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Refinement step | Cycle: final / Resolution: 1.48→24.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.481→1.519 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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