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Yorodumi- PDB-4yxm: Structure of Thermotoga maritima DisA D75N mutant with reaction p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yxm | |||||||||
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Title | Structure of Thermotoga maritima DisA D75N mutant with reaction product c-di-AMP | |||||||||
Components | DNA integrity scanning protein DisA | |||||||||
Keywords | DNA BINDING PROTEIN / c-di-AMP synthesis / DAC domain / Inhibitor / pre-reaction state / TRANSFERASE | |||||||||
Function / homology | Function and homology information diadenylate cyclase activity / diadenylate cyclase / adenylate cyclase activity / DNA repair / DNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Mueller, M. / Deimling, T. / Hopfner, K.-P. / Witte, G. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Biochem.J. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yxm.cif.gz | 297.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yxm.ent.gz | 238.8 KB | Display | PDB format |
PDBx/mmJSON format | 4yxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yxm_validation.pdf.gz | 904.5 KB | Display | wwPDB validaton report |
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Full document | 4yxm_full_validation.pdf.gz | 911.3 KB | Display | |
Data in XML | 4yxm_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 4yxm_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/4yxm ftp://data.pdbj.org/pub/pdb/validation_reports/yx/4yxm | HTTPS FTP |
-Related structure data
Related structure data | 4yvzC 4yxjC 3c1zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42763.000 Da / Num. of mol.: 2 / Mutation: D75N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: disA, TM_0200 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9WY43, diadenylate cyclase #2: Chemical | ChemComp-2BA / ( | #3: Chemical | ChemComp-MPD / ( | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.95 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 30% (v/v) MPD, 200mM Ammonium acetate, 100mM Tris-HCl PH range: 8.0-8.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 47778 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 13 % / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3c1z Resolution: 2.25→49.279 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.41 / 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: 2.25→49.279 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: 13.7191 Å / Origin y: -37.1844 Å / Origin z: -39.5219 Å
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Refinement TLS group | Selection details: all |