[English] 日本語
Yorodumi- PDB-3kb2: Crystal Structure of YorR protein in complex with phosphorylated ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kb2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of YorR protein in complex with phosphorylated GDP from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR256 | ||||||
Components | SPBc2 prophage-derived uncharacterized protein yorR | ||||||
Keywords | structural genomics / unknown function / alpha-beta protein. / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information dUDP biosynthetic process / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Forouhar, F. / Friedman, D. / Seetharaman, J. / Janjua, J. / Xiao, R. / Cunningham, K. / Ma, L. / Ho, C. / Everett, J.K. / Nair, R. ...Forouhar, F. / Friedman, D. / Seetharaman, J. / Janjua, J. / Xiao, R. / Cunningham, K. / Ma, L. / Ho, C. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target SR256 Authors: Forouhar, F. / Friedman, D. / Seetharaman, J. / Janjua, J. / Xiao, R. / Cunningham, K. / Ma, L. / Ho, C. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3kb2.cif.gz | 83.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3kb2.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kb2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3kb2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3kb2_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 3kb2_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/3kb2 ftp://data.pdbj.org/pub/pdb/validation_reports/kb/3kb2 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20257.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU20280, yorR / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: O31896 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.65 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 100 mM cacodylic acid, 14% PEG 8k, and 240 mM magnesium acetate., VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97925 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 6, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 39631 / Num. obs: 39552 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.063 / Net I/σ(I): 14.93 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.38 / Num. unique all: 3969 / Rsym value: 0.348 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.2→19.61 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 318670.812 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.87 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.4 Å2
| ||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.61 Å
| ||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
|