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- PDB-7z67: Crystal structure of the tandem kinase & triphosphate tunnel meta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z67 | ||||||
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Title | Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with a adenosine nucleotide analog. | ||||||
![]() | Inorganic pyrophosphatase TTM1 | ||||||
![]() | UNKNOWN FUNCTION / triphosphate tunnel metalloenzyme / uridine kinase / cytidine kinase / mitochondrial protein | ||||||
Function / homology | ![]() regulation of leaf senescence / pyrophosphatase activity / inorganic diphosphatase / inorganic diphosphate phosphatase activity / defense response / kinase activity / mitochondrial outer membrane / membrane => GO:0016020 / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hothorn, M. / Martinez, J. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Structural and biological insight into the plant unique multimodular triphosphosphate tunnel metalloenzymes of Arabidopsis thaliana Authors: Pesquera, M. / Martinez, J. / Wang, K. / Hofmann, M. / Loubery, S. / Steensma, P. / Hothorn, M. / Fitzpatrick, T.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 | ![]() | 207.2 KB | Display | ![]() |
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PDB format | ![]() | 145.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 864.5 KB | Display | ![]() |
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Full document | ![]() | 867.2 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z66C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45613.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 9 molecules ![](data/chem/img/CIT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CIT / |
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#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-ACP / |
#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-NA / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.55 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 8,000/20% ethylene glycol, 0.1 M carboxylic acids, 0.1 M Tris, pH 8.5, based on Morpheus condition G10 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→46.69 Å / Num. obs: 37785 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 19.2 % / Biso Wilson estimate: 77.75 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.164 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.65→2.8 Å / Redundancy: 19 % / Num. unique obs: 6002 / CC1/2: 0.516 / Rrim(I) all: 2.796 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→46.69 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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