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- PDB-6ewz: 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: 6ewz | ||||||
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Title | Crystal structure of RelP (SAS2) from Staphylococcus aureus bound to AMPCPP and GTP in the pre-catalytic state | ||||||
![]() | GTP pyrophosphokinase | ||||||
![]() | TRANSFERASE / magic spot / (p)ppGpp / small alarmone synthetase / persistence / resistance / MRSA / staphylococcus | ||||||
Function / homology | ![]() GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / kinase activity / phosphorylation / 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 | ![]() | 195.4 KB | Display | ![]() |
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PDB format | ![]() | 155.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ex0C ![]() 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28094.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ywaC, BER48_002454, CEJ93_03805, ERS072738_01254, ERS073583_01544, ERS074020_00750, HMPREF3211_00175 Production host: ![]() ![]() |
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-Non-polymers , 5 types, 106 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/APC.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/APC.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-FE / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-HCl pH8.5 25% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 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: 2.24→63.07 Å / Num. obs: 42049 / % possible obs: 99.93 % / Redundancy: 13.2 % / CC1/2: 1 / Rmerge(I) obs: 0.05537 / Rpim(I) all: 0.01592 / Rrim(I) all: 0.05765 / Net I/σ(I): 24.81 |
Reflection shell | Resolution: 2.24→2.32 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.811 / Mean I/σ(I) obs: 1.42 / CC1/2: 0.664 / Rpim(I) all: 0.5174 / Rrim(I) all: 1.885 / % possible all: 99.88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ded Resolution: 2.24→63.07 Å / Cross valid method: FREE R-VALUE
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→63.07 Å
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LS refinement shell | Resolution: 2.24→2.92 Å
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