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Yorodumi- PDB-7z66: Crystal structure of the tandem kinase & triphosphate tunnel meta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z66 | ||||||
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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 inorganic phosphate and citric acid. | ||||||
Components | Inorganic pyrophosphatase TTM1 | ||||||
Keywords | UNKNOWN FUNCTION / triphosphate tunnel metalloenzyme / uridine kinase / cytidine kinase / mitochondrial protein | ||||||
Function / homology | Function and homology information 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 | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Hothorn, M. / Martinez, J. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z66.cif.gz | 206 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z66.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7z66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/7z66 ftp://data.pdbj.org/pub/pdb/validation_reports/z6/7z66 | HTTPS FTP |
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-Related structure data
Related structure data | 7z67C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45613.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TTM1, At1g73980, F2P9.15 / Plasmid: pMH-HT / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9C9B9, inorganic diphosphatase |
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#2: Chemical | ChemComp-CIT / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.97 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99187 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→46.86 Å / Num. obs: 35969 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 21.2 % / Biso Wilson estimate: 78.54 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.157 / Net I/σ(I): 14.25 |
Reflection shell | Resolution: 2.7→2.87 Å / Redundancy: 21.2 % / Num. unique obs: 5749 / CC1/2: 0.584 / Rrim(I) all: 2.512 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→46.86 Å / SU ML: 0.4617 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9095 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: 95.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→46.86 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: AAAA / Label asym-ID: A
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