+Open data
-Basic information
Entry | Database: PDB / ID: 6ij1 | ||||||
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Title | Crystal structure of a protein from Actinoplanes | ||||||
Components | Prenylcyclase | ||||||
Keywords | TRANSFERASE / prenyltransferase | ||||||
Function / homology | ACETATE ION / IMIDAZOLE / Prenylcyclase Function and homology information | ||||||
Biological species | Actinoplanes teichomyceticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.521 Å | ||||||
Authors | Yang, Z.Z. / Zhang, L.L. / Liu, W.D. / Chen, C.C. / Guo, R.T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2019 Title: Crystal structure of TchmY from Actinoplanes teichomyceticus. Authors: Yang, Z. / Zhang, L. / Yu, X. / Wu, S. / Yang, Y. / Hu, Y. / Li, Q. / Shang, N. / Guo, R.T. / Chen, C.C. / Dai, L. / Liu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ij1.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ij1.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 6ij1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/6ij1 ftp://data.pdbj.org/pub/pdb/validation_reports/ij/6ij1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37388.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria) Gene: tchmY / Plasmid: pET-46EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1B1ESM0 | ||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / | #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: 2.59 Å3/Da / Density % sol: 52.49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.75M K/Na Tartrate, 0.3M Imidazole pH 8.0, 0.4M Nac |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 26, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.52→25 Å / Num. obs: 59674 / % possible obs: 98.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.024 / Rrim(I) all: 0.071 / Χ2: 1.216 / Net I/σ(I): 14.6 / Num. measured all: 533592 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.521→23.718 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.78 Å2 / Biso mean: 22.7697 Å2 / Biso min: 11.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.521→23.718 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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