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- PDB-1ylm: Structure of Cytosolic Protein of Unknown Function YutE from Baci... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ylm | ||||||
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Title | Structure of Cytosolic Protein of Unknown Function YutE from Bacillus subtilis | ||||||
![]() | hypothetical protein BSU32300 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / Bacillus subtilis / hypothetical cytosolic protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | bsu32300-like / Ribonuclease HepT-like / tRNA nuclease HepT-like superfamily / Ribonuclease HepT-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Hydrolases; Acting on ester bonds / Up-down Bundle / Mainly Alpha / Putative RNase YutE![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Hypothetical cytosolic protein YutE from Bacillus subtilis Authors: Binkowski, T.A. / Quartey, P. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.5 KB | Display | ![]() |
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PDB format | ![]() | 59.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.6 KB | Display | ![]() |
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Full document | ![]() | 436.1 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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: 16857.623 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Species: Bacillus subtilis / Strain: subsp. subtilis str. 168 / Gene: YutE / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.5 Details: .075 Tris, 1.5M Ammonium sulfate, 25% glycerol, pH 8.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-1 / Detector: CCD / Date: Nov 14, 2004 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→33.6 Å / Num. all: 31170 / Num. obs: 30664 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.83→1.9 Å / % possible all: 89 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 24.399 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→33.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.832→1.88 Å / Total num. of bins used: 20
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