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- PDB-4edt: The structure of the S. aureus DnaG RNA Polymerase Domain bound t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4edt | ||||||
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Title | The structure of the S. aureus DnaG RNA Polymerase Domain bound to ppGpp and Manganese | ||||||
![]() | DNA primase | ||||||
![]() | transferase/transferase inhibitor / Catalytic Domain / Bacterial / nucleotide / nucleoside triphosphate / nucleoside polyphosphate / protein-ligand complex / transferase / transferase-transferase inhibitor complex | ||||||
Function / homology | ![]() DNA primase DnaG / primosome complex / DNA primase activity / DNA-directed RNA polymerase complex / DNA helicase activity / DNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rymer, R.U. / Solorio, F.A. / Chu, C. / Corn, J.E. / Wang, J.D. / Berger, J.M. | ||||||
![]() | ![]() Title: Binding Mechanism of Metal-NTP Substrates and Stringent-Response Alarmones to Bacterial DnaG-Type Primases. Authors: Rymer, R.U. / Solorio, F.A. / Tehranchi, A.K. / Chu, C. / Corn, J.E. / Keck, J.L. / Wang, J.D. / Berger, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.3 KB | Display | ![]() |
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PDB format | ![]() | 120.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 892.3 KB | Display | ![]() |
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Full document | ![]() | 893.5 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4e2kC ![]() 4edgC ![]() 4edkC ![]() 4edrC ![]() 4edvC ![]() 4ee1C 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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Details | monomer |
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Components
#1: Protein | Mass: 37677.508 Da / Num. of mol.: 1 / Fragment: unp residues 111-436 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O05338, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases | ||
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#2: Chemical | ChemComp-BEN / | ||
#3: Chemical | ChemComp-G4P / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.12 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.15M sodium thiocyanate, 0.1M Bis-Tris, 13% PEG3350, 2% Benzamidine, 2.5 mM ppGpp, 10 mM MnCl2, 1 mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2009 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115 Å / Relative weight: 1 |
Reflection | Resolution: 2.005→131.405 Å / Num. all: 34635 / Num. obs: 34635 / % possible obs: 99.7 % / Redundancy: 8.2 % / Rsym value: 0.075 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.63 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.086 Å2 / ksol: 0.322 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.06 Å2 / Biso mean: 36.3554 Å2 / Biso min: 13.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.005→43.926 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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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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