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Yorodumi- PDB-4ee1: The structure of the S. aureus DnaG RNA Polymerase Domain bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ee1 | ||||||
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Title | The structure of the S. aureus DnaG RNA Polymerase Domain bound to CTP and Manganese | ||||||
Components | DNA primase | ||||||
Keywords | TRANSFERASE / Catalytic Domain / Bacterial / nucleotide / nucleoside triphosphate / nucleoside polyphosphate / protein-ligand complex | ||||||
Function / homology | Function and homology information DNA primase DnaG / DNA primase activity / primosome complex / DNA-directed RNA polymerase complex / DNA helicase activity / DNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Rymer, R.U. / Solorio, F.A. / Chu, C. / Corn, J.E. / Wang, J.D. / Berger, J.M. | ||||||
Citation | Journal: Structure / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ee1.cif.gz | 150.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ee1.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ee1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/4ee1 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/4ee1 | HTTPS FTP |
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-Related structure data
Related structure data | 4e2kC 4edgC 4edkC 4edrC 4edtC 4edvC 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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Unit cell |
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Details | monomer |
-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.) Staphylococcus aureus (bacteria) / Gene: dnaG / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon+ References: UniProt: O05338, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases | ||||
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#2: Chemical | ChemComp-CTP / | ||||
#3: Chemical | #4: Chemical | ChemComp-BEN / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.03 % |
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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 CTP, 5 mM MnCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.02→49.749 Å / Num. all: 32386 / Num. obs: 32386 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Redundancy: 11.4 % / Rsym value: 0.112 / Net I/σ(I): 14.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→49.749 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.25 / σ(F): 1.49 / Phase error: 19.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.879 Å2 / ksol: 0.334 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.02→49.749 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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