+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ktg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a C. elegans Ap4A Hydrolase Binary Complex | ||||||
![]() | Diadenosine Tetraphosphate Hydrolase | ||||||
![]() | HYDROLASE / Nudix / AMP / Magnesium cluster | ||||||
Function / homology | ![]() 5-phosphoribosyl 1-pyrophosphate pyrophosphatase activity / diadenosine tetraphosphate catabolic process / Detoxification of Reactive Oxygen Species / AMP biosynthetic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / ADP biosynthetic process / ribose phosphate metabolic process / ATP biosynthetic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / apoptotic process / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bailey, S. / Sedelnikova, S.E. / Blackburn, G.M. / Abdelghany, H.M. / Baker, P.J. / McLennan, A.G. / Rafferty, J.B. | ||||||
![]() | ![]() Title: The crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms Authors: Bailey, S. / Sedelnikova, S.E. / Blackburn, G.M. / Abdelghany, H.M. / Baker, P.J. / McLennan, A.G. / Rafferty, J.B. #1: ![]() Title: Crystallization of a Complex of Caenorhabditis elegans Diadenosine Tertaphosphate Hydrolase and a Non-Hydrolysable Substrate-Analogue, AppCH2ppA Authors: Bailey, S. / Sedelnikova, S.E. / Blackburn, G.M. / Abdelghany, A.G. / McLennan, A.G. / Rafferty, J.B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 78.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 55.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 460.1 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kt9SC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 15913.135 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9U2M7, bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) |
---|
-Non-polymers , 5 types, 318 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-AMP / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.15 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 4000, Magnesium chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 43 % | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 4, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 62050 / Num. obs: 24019 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.84 Å / % possible all: 96.4 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 97 % / Num. measured all: 62050 / Rmerge(I) obs: 0.097 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / % possible obs: 96.5 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KT9 Resolution: 1.8→19 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.983 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.135 / Stereochemistry target values: Engh & Huber / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.117 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | T33: 0.0016 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 18 Å / Rfactor obs: 0.189 / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.288 / Rfactor Rwork: 0.194 / Rfactor obs: 0.194 |