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- PDB-4jd0: Structure of the inositol-1-phosphate CTP transferase from T. mar... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jd0 | ||||||
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Title | Structure of the inositol-1-phosphate CTP transferase from T. maritima. | ||||||
![]() | Nucleotidyl transferase | ||||||
![]() | TRANSFERASE / alpha/beta motif of sugar nucleotidyltransferase | ||||||
Function / homology | ![]() Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / biosynthetic process / nucleotidyltransferase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Stec, B. | ||||||
![]() | ![]() Title: Structure of the inositol-1-phosphate cytidylyltransferase from Thermotoga maritima. Authors: Kurnasov, O.V. / Luk, H.J. / Roberts, M.F. / Stec, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.1 KB | Display | ![]() |
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PDB format | ![]() | 106.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 828.7 KB | Display | ![]() |
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Full document | ![]() | 835.5 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qqx S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28389.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 255 molecules ![](data/chem/img/1KH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-1KH / | ||||||
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#3: Chemical | ChemComp-CL / | ||||||
#4: Chemical | ChemComp-NA / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1.8 2.0 M ammonium phosphate and 100 mM LiCl buffered at pH 8.5 with 100 mM Tris, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 17, 2009 |
Radiation | Monochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→115.47 Å / Num. all: 38500 / Num. obs: 38500 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.41 / Num. unique all: 1287 / % possible all: 63.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2QQX ![]() 2qqx Resolution: 1.8→115.47 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.877 / SU ML: 0.052 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 31.767 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→115.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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