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- PDB-6fgk: Crystal structure of the small alarmone synthethase 2 from Bacill... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fgk | ||||||
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Title | Crystal structure of the small alarmone synthethase 2 from Bacillus subtilis | ||||||
![]() | GTP pyrophosphokinase YwaC | ||||||
![]() | TRANSFERASE / Stringent response / alarmone / SAS2 / RelP | ||||||
Function / homology | ![]() GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / kinase activity / GTP binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bange, G. / Vogt, M. / Steinchen, W. / Altegoer, F. | ||||||
![]() | ![]() Title: Structural and mechanistic divergence of the small (p)ppGpp synthetases RelP and RelQ. Authors: Steinchen, W. / Vogt, M.S. / Altegoer, F. / Giammarinaro, P.I. / Horvatek, P. / Wolz, C. / 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 | ![]() | 157.9 KB | Display | ![]() |
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PDB format | ![]() | 126.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.4 KB | Display | ![]() |
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Full document | ![]() | 457.9 KB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fgjC ![]() 6fgxC ![]() 5decS 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: 24638.586 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: ywaC, BSU38480, ipa-7d / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES pH 9.5, 30% (w/v) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→47.28 Å / Num. obs: 16011 / % possible obs: 92.2 % / Redundancy: 4.1 % / CC1/2: 0.98 / Rmerge(I) obs: 0.169 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 3.2→3.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1561 / CC1/2: 0.72 / % possible all: 92.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DEC Resolution: 3.2→46.281 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→46.281 Å
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Refine LS restraints |
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LS refinement shell |
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