[English] 日本語
Yorodumi- PDB-1ylm: Structure of Cytosolic Protein of Unknown Function YutE from Baci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ylm | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Cytosolic Protein of Unknown Function YutE from Bacillus subtilis | ||||||
Components | hypothetical protein BSU32300 | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83 Å | ||||||
Authors | Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Hypothetical cytosolic protein YutE from Bacillus subtilis Authors: Binkowski, T.A. / Quartey, P. / Joachimiak, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ylm.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ylm.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ylm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ylm_validation.pdf.gz | 434.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ylm_full_validation.pdf.gz | 436.1 KB | Display | |
Data in XML | 1ylm_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 1ylm_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/1ylm ftp://data.pdbj.org/pub/pdb/validation_reports/yl/1ylm | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 16857.623 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Species: Bacillus subtilis / Strain: subsp. subtilis str. 168 / Gene: YutE / Production host: Escherichia coli (E. coli) / Strain (production host): 168 / References: UniProt: O32126 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.11 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.83→33.6 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→33.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.832→1.88 Å / Total num. of bins used: 20
|