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- PDB-6ex0: Crystal structure of RelP (SAS2) from Staphylococcus aureus bound... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ex0 | |||||||||
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Title | Crystal structure of RelP (SAS2) from Staphylococcus aureus bound to pppGpp in the post-catalytic state | |||||||||
![]() | GTP pyrophosphokinase | |||||||||
![]() | TRANSFERASE / stringent response / (p)ppGpp / persistence / small alarmone synthetase | |||||||||
Function / homology | ![]() GTP diphosphokinase activity / GTP diphosphokinase / guanosine tetraphosphate biosynthetic process / kinase activity / GTP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Manav, M.C. / Brodersen, D.E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for (p)ppGpp synthesis by theStaphylococcus aureussmall alarmone synthetase RelP. Authors: Manav, M.C. / Beljantseva, J. / Bojer, M.S. / Tenson, T. / Ingmer, H. / Hauryliuk, V. / Brodersen, D.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.2 KB | Display | ![]() |
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PDB format | ![]() | 146.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ewzC ![]() 5dedS 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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Unit cell |
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Components
#1: Protein | Mass: 28094.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ywaC, AB454_12730, AB466_12625, AB478_12605, AB526_12980, AFO97_10970, AFP37_10975, EP54_00695, EQ90_03295, ERS072738_01254, ERS074020_00750, HMPREF3211_00175 Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-FE2 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Hepes-Na pH7.0 0.2M Sodium thiocyanate 40% pentaerythriol propoxylate (5/4 PO/OH) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→53.7 Å / Num. obs: 133228 / % possible obs: 99.31 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.07323 / Rpim(I) all: 0.03043 / Rrim(I) all: 0.07981 / Net I/σ(I): 12.63 |
Reflection shell | Resolution: 2.78→2.879 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.048 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 10390 / CC1/2: 0.53 / Rpim(I) all: 0.4922 / Rrim(I) all: 1.168 / % possible all: 93.11 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DED Resolution: 2.78→53.7 Å / Cross valid method: FREE R-VALUE
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||
Displacement parameters | Biso mean: 88.77 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.78→53.7 Å
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LS refinement shell | Resolution: 2.78→2.92 Å /
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