[English] 日本語
![](img/lk-miru.gif)
- PDB-3gxv: Three-dimensional structure of N-terminal domain of DnaB Helicase... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3gxv | ||||||
---|---|---|---|---|---|---|---|
Title | Three-dimensional structure of N-terminal domain of DnaB Helicase from Helicobacter pylori and its interactions with primase | ||||||
![]() | (Replicative DNA helicase) x 3 | ||||||
![]() | HYDROLASE/REPLICATION / Hexameric helicase / Helicobacter pylori / primase / replication / ATP-binding / Autocatalytic cleavage / DNA replication / DNA-binding Hydrolase / Nucleotide-binding / Primosome / DNA-binding / Helicase / Hydrolase / HYDROLASE-REPLICATION COMPLEX | ||||||
Function / homology | ![]() primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kashav, T. / Nitharwal, R. / Syed, A.A. / Gabdoulkhakov, A. / Saenger, W. / Dhar, K.S. / Gourinath, S. | ||||||
![]() | ![]() Title: Three-dimensional structure of N-terminal domain of DnaB helicase and helicase-primase interactions in Helicobacter pylori Authors: Kashav, T. / Nitharwal, R. / Abdulrehman, S.A. / Gabdoulkhakov, A. / Saenger, W. / Dhar, S.K. / Gourinath, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 73.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 56.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 462.2 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2r5uS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 14291.337 Da / Num. of mol.: 2 / Fragment: N-terminal domain, residues 1-121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O25916, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #2: Protein/peptide | | Mass: 2489.978 Da / Num. of mol.: 1 / Fragment: residues 101-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O25916, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #3: Protein/peptide | | Mass: 2976.450 Da / Num. of mol.: 1 / Fragment: residues 98-123 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O25916, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.45 Å3/Da / Density % sol: 72.37 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Bis Tris, Ammonium Sulphate, Sodium malonate, Peg 550MME, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 18, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.32 Å / Num. obs: 30563 / Redundancy: 5.32 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.095 / Net I/σ(I): 9.78 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.35 / Num. unique all: 6637 / Rsym value: 0.575 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2r5u Resolution: 2.2→19.32 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 52275.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.3451 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|