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Yorodumi- PDB-5ded: Crystal structure of the small alarmone synthethase 1 from Bacill... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ded | ||||||
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Title | Crystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to its product pppGpp | ||||||
Components | GTP pyrophosphokinase YjbM | ||||||
Keywords | TRANSFERASE / (p)ppGpp / alarmone / stringent response / allosteric regulator | ||||||
Function / homology | Function and homology information GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / kinase activity / phosphorylation / GTP binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis PY79 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.942 Å | ||||||
Authors | Steinchen, W. / Schuhmacher, J.S. / Altegoer, F. / Bange, G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ded.cif.gz | 329.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ded.ent.gz | 269.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ded.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/5ded ftp://data.pdbj.org/pub/pdb/validation_reports/de/5ded | HTTPS FTP |
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-Related structure data
Related structure data | 5decSC 5f2vC 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: 25629.303 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis PY79 (bacteria) / Strain: 168 / Gene: yjbM, BSU11600 / Plasmid: pET24d(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O31611, GTP diphosphokinase #2: Chemical | ChemComp-0O2 / #3: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citric acid, pH 4.0, 5% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97934 Å |
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: 2.94→50.6 Å / Num. obs: 51454 / % possible obs: 96.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 5.8 |
Reflection shell | Rmerge(I) obs: 0.273 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DEC Resolution: 2.942→50.567 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.66 / 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: 2.942→50.567 Å
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Refine LS restraints |
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LS refinement shell |
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