[English] 日本語
Yorodumi- PDB-3on1: The structure of a protein with unknown function from Bacillus ha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3on1 | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of a protein with unknown function from Bacillus halodurans C | ||||||
Components | BH2414 protein | ||||||
Keywords | structural genomics / unknown function / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Fan, Y. / Kagan, O. / Savchenko, A. / Joachimiak, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The structure of a protein with unknown function from Bacillus halodurans C Authors: Fan, Y. / Kagan, O. / Savchenko, A. / Joachimiak, A. / Edwards, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3on1.cif.gz | 54.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3on1.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 3on1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3on1_validation.pdf.gz | 418.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3on1_full_validation.pdf.gz | 421.5 KB | Display | |
Data in XML | 3on1_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 3on1_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/3on1 ftp://data.pdbj.org/pub/pdb/validation_reports/on/3on1 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11032.677 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH2414 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KA76 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.95 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: Na formate 4M, 221NDSB 0.3M, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Mar 4, 2010 / Details: mirror |
Radiation | Monochromator: Si111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 11377 / Num. obs: 11377 / % possible obs: 97.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 58.76 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 11.34 / Num. unique all: 465 / % possible all: 81.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.65→37.69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.442 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R Free: 0.104 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.26 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→37.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.655→1.698 Å / Total num. of bins used: 20
|