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- PDB-4yvz: Structure of Thermotoga maritima DisA in complex with 3'-dATP/Mn2+ -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yvz | |||||||||
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Title | Structure of Thermotoga maritima DisA in complex with 3'-dATP/Mn2+ | |||||||||
![]() | DNA integrity scanning protein DisA | |||||||||
![]() | DNA BINDING PROTEIN / c-di-AMP synthesis / DAC domain / Inhibitor / pre-reaction state / TRANSFERASE | |||||||||
Function / homology | ![]() diadenylate cyclase activity / diadenylate cyclase / adenylate cyclase activity / DNA repair / DNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mueller, M. / Deimling, T. / Hopfner, K.-P. / Witte, G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of the diadenylate cyclase reaction of DNA-integrity scanning protein A (DisA) and its inhibition by 3'-dATP. Authors: Muller, M. / Deimling, T. / Hopfner, K.P. / Witte, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 295.6 KB | Display | ![]() |
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PDB format | ![]() | 239.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 27.3 KB | Display | |
Data in CIF | ![]() | 37.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yxjC ![]() 4yxmC ![]() 3c1zS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 42763.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.85 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 30% (v/v) MPD, 200 mM ammoniumacetate, 100 mM Tris-HCl PH range: 8.0-8.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23953 Å / Relative weight: 1 |
Reflection | Resolution: 2.495→168.8 Å / Num. obs: 65492 / % possible obs: 99.6 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.495→2.56 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 2.8 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3c1z Resolution: 2.495→168.79 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.495→168.79 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 13.1059 Å / Origin y: -36.6604 Å / Origin z: 43.8695 Å
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Refinement TLS group | Selection details: all |