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- PDB-6vqp: Structure of CalU17 from the Calicheamicin Biosynthesis Pathway o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vqp | ||||||||||||
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Title | Structure of CalU17 from the Calicheamicin Biosynthesis Pathway of Micromonospora echinospora | ||||||||||||
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![]() | UNKNOWN FUNCTION / Enediyne biosynthetic pathway / Calicheamicin Biosynthesis | ||||||||||||
Function / homology | Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1 / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / metal ion binding / CalU17![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Kosgei, A.J. / Miller, M.D. / Xu, W. / Van Lanen, S.G. / Thorson, J.S. / Phillips Jr., G.N. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of DynF from the Dynemicin Biosynthesis Pathway of Micromonospora chersina Authors: Kosgei, A.J. / Miller, M.D. / Xu, W. / Van Lanen, S.G. / Thorson, J.S. / Phillips Jr., G.N. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.6 KB | Display | ![]() |
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PDB format | ![]() | 101.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 263.4 KB | Display | ![]() |
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Full document | ![]() | 263.4 KB | Display | |
Data in XML | ![]() | 1.3 KB | Display | |
Data in CIF | ![]() | 6.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1y1eS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 37235.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Protein/peptide | Mass: 2051.233 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Chain Q, is the N-terminus tag from a neighboring chain. Due to the disorderd gap from residue -3 to 16, it is not clear which of two possible crystallographic symmetry transformations would ...Details: Chain Q, is the N-terminus tag from a neighboring chain. Due to the disorderd gap from residue -3 to 16, it is not clear which of two possible crystallographic symmetry transformations would transform chain Q to the position of the N-terminus of chain A. It is likely either Y+1/2, -X+1/2, Z+1/4 or -Y, -X+1, -Z+1/2 Source: (gene. exp.) ![]() ![]() ![]() | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.33 % Description: It took a month fro the crystals to grow. The size of the crystals were about 70 microns length, width and height. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Bis-Tris pH 6.5 20% w/v PEG 1500 Temp details: Set the crystallization trays at room temperature then incubated at 4 degrees |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→48.39 Å / Num. obs: 23026 / % possible obs: 99.8 % / Redundancy: 12.622 % / Biso Wilson estimate: 38.227 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.111 / Χ2: 1.06 / Net I/σ(I): 16.03 / Num. measured all: 290624 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1y1e Resolution: 2→48.39 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 151.11 Å2 / Biso mean: 42.2929 Å2 / Biso min: 22.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→48.39 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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