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- PDB-5w35: Crystal structure of the RNA polymerase domain (RPD) of Mycobacte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w35 | ||||||
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Title | Crystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis primase DnaG in complex with a double-stranded DNA oligomer with a 1-nucleotide overhang | ||||||
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![]() | TRANSFERASE/DNA / DNA replication / replisome / TOPRIM fold / DNA binding / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() DNA primase DnaG / primosome complex / DNA primase activity / DNA replication, synthesis of primer / DNA-directed RNA polymerase complex / DNA binding / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hou, C. / Tsodikov, O.V. | ||||||
![]() | ![]() Title: Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events. Authors: Hou, C. / Biswas, T. / Tsodikov, O.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.1 KB | Display | ![]() |
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PDB format | ![]() | 106 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.7 KB | Display | ![]() |
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Full document | ![]() | 448.6 KB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w33C ![]() 5w34SC ![]() 5w36C C: citing same article ( S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 35450.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: dnaG, Rv2343c, MTCY98.12c / Production host: ![]() ![]() References: UniProt: P9WNW1, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: DNA chain | | Mass: 3574.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 4056.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.89 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM Hepes pH 7.0, 6% PEG 4000, 5 mM SrCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 12200 / % possible obs: 99.8 % / Redundancy: 4.4 % / Net I/σ(I): 24 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5W34 Resolution: 3.31→35 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 37.379 / SU ML: 0.579 / Cross valid method: THROUGHOUT / ESU R Free: 0.619 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: 1 / Resolution: 3.31→35 Å
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Refine LS restraints |
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