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Yorodumi- PDB-6fgj: Crystal structure of the small alarmone synthethase 2 from Staphy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fgj | ||||||
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Title | Crystal structure of the small alarmone synthethase 2 from Staphylococcus aureus | ||||||
Components | GTP pyrophosphokinase | ||||||
Keywords | TRANSFERASE / Stringent response / alarmone / RelP / SAS2 / MRSA | ||||||
Function / homology | Function and homology information GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / kinase activity / phosphorylation Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å | ||||||
Authors | Bange, G. / Steinchen, W. / Vogt, M. / Altegoer, F. | ||||||
Citation | Journal: Sci Rep / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fgj.cif.gz | 177.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fgj.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 6fgj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/6fgj ftp://data.pdbj.org/pub/pdb/validation_reports/fg/6fgj | HTTPS FTP |
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-Related structure data
Related structure data | 6fgkC 6fgxC 5decS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28094.139 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) 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: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8U368, GTP diphosphokinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.24 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris pH 8.5, 0.2 M lithium sulfate, 30% (w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→49.06 Å / Num. obs: 24257 / % possible obs: 99 % / Redundancy: 4.3 % / CC1/2: 1 / Rmerge(I) obs: 0.0364 / Net I/σ(I): 20.37 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.58 / Num. unique obs: 10417 / CC1/2: 0.85 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DEC Resolution: 2.251→49.06 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.251→49.06 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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