[English] 日本語
![](img/lk-miru.gif)
- PDB-3oi7: Structure of the structure of the H13A mutant of Ykr043C in compl... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3oi7 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the structure of the H13A mutant of Ykr043C in complex with sedoheptulose-1,7-bisphosphate | ||||||
![]() | Uncharacterized protein YKR043C | ||||||
![]() | HYDROLASE / beta-furanose / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / alpha-beta / sedoheptulose-1 / 7-bisphosphatase / phosphatase | ||||||
Function / homology | ![]() sedoheptulose-bisphosphatase / sedoheptulose-bisphosphatase activity / ribose phosphate biosynthetic process / oxidoreductase activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Singer, A.U. / Xu, X. / Dong, A. / Cui, H. / Clasquin, M.F. / Caudy, A.A. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Yakunin, A.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Riboneogenesis in yeast. Authors: Clasquin, M.F. / Melamud, E. / Singer, A. / Gooding, J.R. / Xu, X. / Dong, A. / Cui, H. / Campagna, S.R. / Savchenko, A. / Yakunin, A.F. / Rabinowitz, J.D. / Caudy, A.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 227.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 182.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3f3kS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-
Components
-Protein / Sugars , 2 types, 8 molecules ABCD![](data/chem/img/OI7.gif)
![](data/chem/img/OI7.gif)
#1: Protein | Mass: 33661.906 Da / Num. of mol.: 4 / Mutation: H13A Source method: isolated from a genetically manipulated source Details: no TEV cleavage, but limiting amounts of trypsin added during crystallization Source: (gene. exp.) ![]() ![]() Strain: S288C / Gene: YKR043C / Plasmid: P15TvLic / Production host: ![]() ![]() #2: Sugar | ChemComp-OI7 / |
---|
-Non-polymers , 5 types, 264 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.72 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Hepes 7.5, 10%Iso-propnal, 22%PEG4K, 4%Glycerol, 0.03 mg/ml trypsin, soaking 10min in well solution w/10mM sedoheptulose. Cryoprotected in Paratone-N oil, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 22, 2010 / Details: mirrors |
Radiation | Monochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 69828 / Num. obs: 57671 / % possible obs: 82.6 % / Observed criterion σ(F): -3 / Redundancy: 1.6 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.88 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.112 / Mean I/σ(I) obs: 3.02 / Num. unique all: 1286 / % possible all: 36.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB 3F3K molecule A protein atoms Resolution: 2.4→27.5 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.891 / SU B: 7.448 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.503 / ESU R Free: 0.284 / 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: 23.929 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→27.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 2082 / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
|