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- PDB-4im9: Cystal structure of DnaG primase C-terminal domain from Vibrio ch... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4im9 | ||||||
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Title | Cystal structure of DnaG primase C-terminal domain from Vibrio cholerae | ||||||
![]() | DNA primase | ||||||
![]() | TRANSFERASE / helicase-primase complex / DNA replication / Hair pin helix / helicase binding | ||||||
Function / homology | DNAb Helicase; Chain A / DNAb Helicase; Chain A / Orthogonal Bundle / Mainly Alpha / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Abdul Rehman, S.A. / Tarique, K.F. / Gourinath, S. | ||||||
![]() | ![]() Title: Cystal structure of DnaG primase C-terminal domain from Vibrio cholerae Authors: Abdul Rehman, S.A. / Tarique, K.F. / Gourinath, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.1 KB | Display | ![]() |
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PDB format | ![]() | 72.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17706.951 Da / Num. of mol.: 3 / Fragment: Primase C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: C3LX44, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.97 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Sodium cacodylate trihydrate (pH 6.5), 0.2 M MgCl2, 30% W/v PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 21, 2012 / Details: bent collimating mirror and toroid |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→66.326 Å / Num. all: 25083 / Num. obs: 25046 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1189 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.888 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3683 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→66.326 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.457→2.52 Å / Total num. of bins used: 20
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