+Open data
-Basic information
Entry | Database: PDB / ID: 4e2k | ||||||
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Title | The structure of the S. aureus DnaG RNA Polymerase Domain | ||||||
Components | DNA primasePrimase | ||||||
Keywords | TRANSFERASE / Catalytic Domain / Bacterial / apo protein | ||||||
Function / homology | Function and homology information DNA primase DnaG / primosome complex / DNA primase activity / DNA helicase activity / DNA-directed RNA polymerase complex / DNA binding / zinc ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Rymer, R.U. / Solorio, F.A. / Clement, 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 | 4e2k.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e2k.ent.gz | 118.9 KB | Display | PDB format |
PDBx/mmJSON format | 4e2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/4e2k ftp://data.pdbj.org/pub/pdb/validation_reports/e2/4e2k | HTTPS FTP |
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-Related structure data
Related structure data | 4edgC 4edkC 4edrC 4edtC 4edvC 4ee1C 1ddeS 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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Unit cell |
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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.) Staphylococcus aureus (bacteria) / Gene: dnaG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon+ References: UniProt: O05338, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases | ||
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#2: Chemical | #3: 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: 3.38 Å3/Da / Density % sol: 63.65 % |
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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, 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 315 / 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: 2.15→50 Å / Num. all: 28064 / Num. obs: 28010 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 30.5 | |||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DDE Resolution: 2.15→30.433 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 20.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.271 Å2 / ksol: 0.319 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→30.433 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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