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- PDB-5f2v: Crystal structure of the small alarmone synthethase 1 from Bacill... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5f2v | |||||||||
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Title | Crystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to AMPCPP | |||||||||
![]() | GTP pyrophosphokinase YjbM | |||||||||
![]() | TRANSFERASE / (p)ppGpp / alarmone / stringent response / allosteric regulator | |||||||||
Function / homology | ![]() GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / kinase activity / phosphorylation / GTP binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Steinchen, W. / Schuhmacher, J.S. / Altegoer, F. / Bange, G. | |||||||||
![]() | ![]() Title: Catalytic mechanism and allosteric regulation of an oligomeric (p)ppGpp synthetase by an alarmone. Authors: Steinchen, W. / Schuhmacher, J.S. / Altegoer, F. / Fage, C.D. / Srinivasan, V. / Linne, U. / Marahiel, M.A. / Bange, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 470.8 KB | Display | ![]() |
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PDB format | ![]() | 385.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.4 MB | Display | ![]() |
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Full document | ![]() | 4.5 MB | Display | |
Data in XML | ![]() | 92.5 KB | Display | |
Data in CIF | ![]() | 116.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5decSC ![]() 5dedC 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24497.084 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-APC / ![]() Source method: isolated from a genetically manipulated source Formula: C11H18N5O12P3 / Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M KSCN, 20% (W/V) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.31 Å / Num. obs: 78602 / % possible obs: 0.995 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 2.8 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.8 / % possible all: 0.895 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DEC Resolution: 2.8→48.31 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.05 / 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: 2.8→48.31 Å
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Refine LS restraints |
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LS refinement shell |
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